CmoCh19G003470 (gene) Cucurbita moschata (Rifu) v1

Overview


Name	CmoCh19G003470
Type	gene
Organism	Cucurbita moschata (Cucurbita moschata (Rifu) v1)
Description	Retrovirus-related Pol polyprotein from transposon RE1
Location	Cmo_Chr19: 2891313 .. 2891645 (+)
RNA-Seq Expression	CmoCh19G003470
Synteny	CmoCh19G003470

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: exonCDSpolypeptide

Hold the cursor over a type above to highlight its positions in the sequence below.

ATGGCTATTGTCGTTGGTCTCTCTACTGCACGTGATGTTCGGCTTGCGTTGGAAACTGCGTTCAACCATCATTCGAAAGCTTGTGAACTGAGACTCAAGGATGACTTGCAATTGATGAAACATGGCATCAAACCTGTTGCTGCGTATGCCCGTGCCTTCAAAAAAATTTGTGACCAACTTTATGCCATTGGCAGACCCGTCGAGGATATTGATAAAGTGCACTGGTTCCTTCGTGGACTTGGCACAGAATTTTCAGCTTTTTCTACTGCTCAGATAGCTCTCACACCTATCCCTTGTTTTGTAGATTTAGTCTCTAAAGTTGAAATTTTTTAG

mRNA sequence

ATGGCTATTGTCGTTGGTCTCTCTACTGCACGTGATGTTCGGCTTGCGTTGGAAACTGCGTTCAACCATCATTCGAAAGCTTGTGAACTGAGACTCAAGGATGACTTGCAATTGATGAAACATGGCATCAAACCTGTTGCTGCGTATGCCCGTGCCTTCAAAAAAATTTGTGACCAACTTTATGCCATTGGCAGACCCGTCGAGGATATTGATAAAGTGCACTGGTTCCTTCGTGGACTTGGCACAGAATTTTCAGCTTTTTCTACTGCTCAGATAGCTCTCACACCTATCCCTTGTTTTGTAGATTTAGTCTCTAAAGTTGAAATTTTTTAG

Coding sequence (CDS)

ATGGCTATTGTCGTTGGTCTCTCTACTGCACGTGATGTTCGGCTTGCGTTGGAAACTGCGTTCAACCATCATTCGAAAGCTTGTGAACTGAGACTCAAGGATGACTTGCAATTGATGAAACATGGCATCAAACCTGTTGCTGCGTATGCCCGTGCCTTCAAAAAAATTTGTGACCAACTTTATGCCATTGGCAGACCCGTCGAGGATATTGATAAAGTGCACTGGTTCCTTCGTGGACTTGGCACAGAATTTTCAGCTTTTTCTACTGCTCAGATAGCTCTCACACCTATCCCTTGTTTTGTAGATTTAGTCTCTAAAGTTGAAATTTTTTAG

Protein sequence

MAIVVGLSTARDVRLALETAFNHHSKACELRLKDDLQLMKHGIKPVAAYARAFKKICDQLYAIGRPVEDIDKVHWFLRGLGTEFSAFSTAQIALTPIPCFVDLVSKVEIF

Homology

[Close]

BLAST of CmoCh19G003470 vs. ExPASy TrEMBL
Match: A0A438DCU0 (Retrovirus-related Pol polyprotein from transposon RE1 OS=Vitis vinifera OX=29760 GN=RE1_2775 PE=4 SV=1)

HSP 1 Score: 177.2 bits (448), Expect = 3.8e-41
Identity = 85/110 (77.27%), Postives = 96/110 (87.27%), Query Frame = 0


Query: 1   MAIVVGLSTARDVRLALETAFNHHSKACELRLKDDLQLMKHGIKPVAAYARAFKKICDQL 60
           +A+VVGLSTAR+V LALE  FNHHSKA ELRLKDDLQLMK G KPVA YAR FK +C+QL
Sbjct: 92  IAVVVGLSTAREVWLALENTFNHHSKARELRLKDDLQLMKRGTKPVAEYARTFKTLCNQL 151

Query: 61  YAIGRPVEDIDKVHWFLRGLGTEFSAFSTAQIALTPIPCFVDLVSKVEIF 111
           +AIGRPVED DKVHWFLRGLGT+FS+FSTAQ++LTP+P F DLVSK E F
Sbjct: 152 HAIGRPVEDTDKVHWFLRGLGTDFSSFSTAQMSLTPLPYFADLVSKAESF 201

[Close]

BLAST of CmoCh19G003470 vs. ExPASy TrEMBL
Match: A0A438EBA0 (Retrovirus-related Pol polyprotein from transposon TNT 1-94 OS=Vitis vinifera OX=29760 GN=POLX_2065 PE=4 SV=1)

HSP 1 Score: 175.6 bits (444), Expect = 1.1e-40
Identity = 84/110 (76.36%), Postives = 95/110 (86.36%), Query Frame = 0


Query: 1   MAIVVGLSTARDVRLALETAFNHHSKACELRLKDDLQLMKHGIKPVAAYARAFKKICDQL 60
           + +VVGLSTAR+V LALE  F+HHSKA ELRLKDDLQLMK G KPVA YAR FK +CDQL
Sbjct: 108 IVVVVGLSTAREVWLALENTFSHHSKARELRLKDDLQLMKRGTKPVAEYARTFKTLCDQL 167

Query: 61  YAIGRPVEDIDKVHWFLRGLGTEFSAFSTAQIALTPIPCFVDLVSKVEIF 111
           +AIGRPVED DKVHWFLRGLGT+FS+FSTAQ++LTP+P F DLVSK E F
Sbjct: 168 HAIGRPVEDTDKVHWFLRGLGTDFSSFSTAQMSLTPLPYFADLVSKAESF 217

[Close]

BLAST of CmoCh19G003470 vs. ExPASy TrEMBL
Match: A0A438IYJ9 (Retrovirus-related Pol polyprotein from transposon RE1 OS=Vitis vinifera OX=29760 GN=RE1_2517 PE=3 SV=1)

HSP 1 Score: 174.9 bits (442), Expect = 1.9e-40
Identity = 84/110 (76.36%), Postives = 95/110 (86.36%), Query Frame = 0


Query: 1   MAIVVGLSTARDVRLALETAFNHHSKACELRLKDDLQLMKHGIKPVAAYARAFKKICDQL 60
           +A+VVGLSTAR+V LALE  F+HHSKA ELRLKDDLQLMK G KPVA YAR FK +CDQL
Sbjct: 185 IAVVVGLSTAREVWLALENTFSHHSKARELRLKDDLQLMKRGTKPVAEYARTFKTLCDQL 244

Query: 61  YAIGRPVEDIDKVHWFLRGLGTEFSAFSTAQIALTPIPCFVDLVSKVEIF 111
           +AIGRPVED DKVHWFLRGLG +FS+FSTAQ++LTP+P F DLVSK E F
Sbjct: 245 HAIGRPVEDTDKVHWFLRGLGPDFSSFSTAQMSLTPLPYFADLVSKAESF 294

[Close]

BLAST of CmoCh19G003470 vs. ExPASy TrEMBL
Match: A5C5R8 (Integrase catalytic domain-containing protein OS=Vitis vinifera OX=29760 GN=VITISV_032383 PE=4 SV=1)

HSP 1 Score: 173.3 bits (438), Expect = 5.5e-40
Identity = 83/110 (75.45%), Postives = 94/110 (85.45%), Query Frame = 0


Query: 1   MAIVVGLSTARDVRLALETAFNHHSKACELRLKDDLQLMKHGIKPVAAYARAFKKICDQL 60
           +A+VVGLSTAR+V LALE  F+HHSKA ELRLKDDLQLMK G KPVA YAR FK +CDQL
Sbjct: 92  IAVVVGLSTAREVWLALENTFSHHSKARELRLKDDLQLMKRGTKPVAEYARTFKTLCDQL 151

Query: 61  YAIGRPVEDIDKVHWFLRGLGTEFSAFSTAQIALTPIPCFVDLVSKVEIF 111
           +AIGRPVED DKVHWF RGLG +FS+FSTAQ++LTP+P F DLVSK E F
Sbjct: 152 HAIGRPVEDTDKVHWFFRGLGPDFSSFSTAQMSLTPLPYFADLVSKAESF 201

[Close]

BLAST of CmoCh19G003470 vs. ExPASy TrEMBL
Match: A0A438FR86 (Retrovirus-related Pol polyprotein from transposon RE1 OS=Vitis vinifera OX=29760 GN=RE1_2860 PE=4 SV=1)

HSP 1 Score: 173.3 bits (438), Expect = 5.5e-40
Identity = 83/110 (75.45%), Postives = 94/110 (85.45%), Query Frame = 0


Query: 1   MAIVVGLSTARDVRLALETAFNHHSKACELRLKDDLQLMKHGIKPVAAYARAFKKICDQL 60
           +A+VVGLSTAR+V LALE  F+HHSKA ELRLKDDLQLMK G KPVA YAR FK +CDQ 
Sbjct: 92  IAVVVGLSTAREVWLALENTFSHHSKARELRLKDDLQLMKRGTKPVAEYARTFKTLCDQF 151

Query: 61  YAIGRPVEDIDKVHWFLRGLGTEFSAFSTAQIALTPIPCFVDLVSKVEIF 111
           +AIGRPVED DKVHWFLRGL T+FS+FSTAQ++LTP+P F DLVSK E F
Sbjct: 152 HAIGRPVEDTDKVHWFLRGLSTDFSSFSTAQMSLTPLPYFADLVSKAESF 201

The following BLAST results are available for this feature:

BLAST of CmoCh19G003470 vs.


Match Name	E-value	Identity	Description

BLAST of CmoCh19G003470 vs. ExPASy TrEMBL


Match Name	E-value	Identity	Description
A0A438DCU0	3.8e-41	77.27	Retrovirus-related Pol polyprotein from transposon RE1 OS=Vitis vinifera OX=2976...	[more]
A0A438EBA0	1.1e-40	76.36	Retrovirus-related Pol polyprotein from transposon TNT 1-94 OS=Vitis vinifera OX...	[more]
A0A438IYJ9	1.9e-40	76.36	Retrovirus-related Pol polyprotein from transposon RE1 OS=Vitis vinifera OX=2976...	[more]
A5C5R8	5.5e-40	75.45	Integrase catalytic domain-containing protein OS=Vitis vinifera OX=29760 GN=VITI...	[more]
A0A438FR86	5.5e-40	75.45	Retrovirus-related Pol polyprotein from transposon RE1 OS=Vitis vinifera OX=2976...	[more]

BLAST of CmoCh19G003470 vs. ExPASy TrEMBL


Match Name	E-value	Identity	Description

InterPro

Analysis Name: InterPro Annotations of Cucurbita moschata (Rifu) v1
Date Performed: 2021-10-25


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
None	No IPR available	PFAM	PF14223	Retrotran_gag_2	coord: 4..90 e-value: 3.3E-10 score: 39.9
None	No IPR available	PANTHER	PTHR47481	FAMILY NOT NAMED	coord: 1..108
None	No IPR available	PANTHER	PTHR47481:SF3	GAG-POLYPEPTIDE OF LTR COPIA-TYPE-RELATED	coord: 1..108

Relationships

The following mRNA feature(s) are a part of this gene:


Feature Name	Unique Name	Type
CmoCh19G003470.1	CmoCh19G003470.1	mRNA

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0015074	DNA integration
biological_process	GO:0006412	translation
cellular_component	GO:0005840	ribosome
molecular_function	GO:0008097	5S rRNA binding
molecular_function	GO:0003735	structural constituent of ribosome
molecular_function	GO:0008270	zinc ion binding