RetrogeneDB ID: retro_cjac_1695

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:7046647..7048122(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SART3
• Ensembl ID: ENSCJAG00000015330
• Aliases: None
• Description: None

Sequence

>retro_cjac_1695
TGCATGATCATGCAGAACTGGGCTAGGATTGAGGCTCGGCTGTGCAGTAACATGCAGAAAGCTCGGGAACTCTGGGATAG
CATCATGACCAGAGAAAACGCCAAGTACGCCAACATGCGGCTAGAGTATTACAACCTGGAGAGGGCACATGTGACACCCA
GCACTGCCGGAAGGCGCTGCACTGGGCCGTCCAGTGCACCAGTGACTACCCAGAGCATGTCTGCGAAGTGTGGCTCACCA
TGGAGAGGACAGAAGGTTCTTTAGAAGATTGGGATATAGCTGTTCAGAAAACTGAAACCCGGTTAGCTCGTGTCAACGAG
CAGAGATTGAAGGCTGCAGAGAAGGAAGCAGCCCTTGTGCAGCAAGAAGAAGAAAAGGCTGAACAACGGAAAAGAGCCCT
GGCTGAGAAGAAAGCACTGAAAAAGAAGAAAAAGACCAGAGGCCCAGATAAGCGCGGAGCAGATGAGGATGATGAGAAGG
AGTGGGGCGATGATGAAGAAGAGCAGCCTTCCAAACGCAGAGGGGTGGAGAACAGCATCCCTGCAGCTGGAGAAGCACAA
AACGTGGAATCAGAAGCAGGGCCCACTGGGAAATGTGCTGTTGTAGATGTGGAGCATTCTTCGAAGCAGAAGGAGAAGGC
AGCCTCCCTGAAAAGGGACATGCCCAAGGTGCTGCAGGACAGCAGCAAGGACAGCATCACCGTCTTTGTCAGCAACCTGC
CCTATAGCATGCAGGAGCGGGATGCGAAGCTCAAGCCGCTCTTCAAGGCCTGTGGGGAGGTGGTCCAGATCCGACCCATC
TTCAGCCACCGTGGGGATTTCCAAGGCTACTGCTATGTGGAGTTTAAAGAAGAGAAATCAGCCCTTCAGGCACTGGAAAT
GGACCGTAAAAGTGTAGAGGGGAGGCCAATGTTTGTTTCCCCCTGTGTGGATAAGAGCAAAAATCCCGATTTTAAGGTGC
TCAGGTACAGCACTTCCCTGGAGAAACACAAGCTGTTCATCTCGGGCCTGCCTTTCTCCTGCACTAAAGAGGAACTAGAG
GAAATCTGTAAGGTTCATGGCACCATGAAGGACCTCAGGCTGGTCACCAATAGGGCTGGCAAACCAAAGGGCCTGGCCTA
TGTAGAGTATGAAAATGAATCCCAGGCGTCGCAGGCTGTGATGAAGATGGACAGCATGACTATCAAAGAGAATGTCATCA
AAGTGGCAATCAGCAACCCTCCTCAGAGGAAGGTTCCAGAGAAGCCAGAGGCCAGGAAGGCATCAGGTGGCCCCATGCCT
TCACCGCAGACATACGGAGCAAGGGGGAAGGGAAGGACGCAGCTGGCTCTACTGCCTCGTGCCCTGCAGTGCCCAAGTGC
TGCAGCTCCTCAGGCCGAGAACGGCCCTGCCCCAGCTCCTGCAGTTGCCACCCCACCAGCCACCGAGGCACCCAAGATGT
CCAATGCCAATTTTGCCAAGCTGTTTCTGAGAAAG

Alignment

ORF - retro_cjac_1695 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.73 %
• Parental protein coverage: 53.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CVIMQNWARIEARLCNNMQKARELWDSIMTRGNAKYANMWLEYYNLERAHG-DTQHCRKALHRAVQCTSD
          C.IMQNWARIEARLC.NMQKARELWDSIMTR.NAKYANM.LEYYNLERAH..DTQHCRKALH.AVQCTSD
Retrocopy CMIMQNWARIEARLCSNMQKARELWDSIMTRENAKYANMRLEYYNLERAHV<DTQHCRKALHWAVQCTSD

Parental  YPEHVCEVLLTMERTEGSLEDWDIAVQKTETRLARVNEQRLKAAEKEAALVQQEEEKAEQRKRARAEKKA
          YPEHVCEV.LTMERTEGSLEDWDIAVQKTETRLARVNEQRLKAAEKEAALVQQEEEKAEQRKRA.AEKKA
Retrocopy YPEHVCEVWLTMERTEGSLEDWDIAVQKTETRLARVNEQRLKAAEKEAALVQQEEEKAEQRKRALAEKKA

Parental  LKKKKKTRGPDKRGADEDDEKEWGDDEEEQPSKRRRVENSIPAAGETQNMESAAGPAGKCAVVDVEPPSK
          LKKKKKTRGPDKRGADEDDEKEWGDDEEEQPSKRR.VENSIPAAGE.QN.ES.AGP.GKCAVVDVE..SK
Retrocopy LKKKKKTRGPDKRGADEDDEKEWGDDEEEQPSKRRGVENSIPAAGEAQNVESEAGPTGKCAVVDVEHSSK

Parental  QKEKAASLKRDMPKVLHDSSKDSITVFVSNLPYSMQEPDAKLKPLFEACGEVVQIRPIFSNRGDFRGYCY
          QKEKAASLKRDMPKVL.DSSKDSITVFVSNLPYSMQE.DAKLKPLF.ACGEVVQIRPIFS.RGDF.GYCY
Retrocopy QKEKAASLKRDMPKVLQDSSKDSITVFVSNLPYSMQERDAKLKPLFKACGEVVQIRPIFSHRGDFQGYCY

Parental  VEFKEEKSALQALEMDRKSVEGRPMFVSPCVDKSKNPDFKVFRYSTSLEKHKLFISGLPFSCTKEELEEI
          VEFKEEKSALQALEMDRKSVEGRPMFVSPCVDKSKNPDFKV.RYSTSLEKHKLFISGLPFSCTKEELEEI
Retrocopy VEFKEEKSALQALEMDRKSVEGRPMFVSPCVDKSKNPDFKVLRYSTSLEKHKLFISGLPFSCTKEELEEI

Parental  CKVHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENVIKVAISNPPQRKVPEKPEAR
          CKVHGT.KDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD.MTIKENVIKVAISNPPQRKVPEKPEAR
Retrocopy CKVHGTMKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDSMTIKENVIKVAISNPPQRKVPEKPEAR

Parental  KASGGPMPSPQTYGARGKGRTQLALLPRALQRPSAAAPQAENGPAPAPAVATPPATEAPKMSNADFAKLF
          KASGGPMPSPQTYGARGKGRTQLALLPRALQ.PSAAAPQAENGPAPAPAVATPPATEAPKMSNA.FAKLF
Retrocopy KASGGPMPSPQTYGARGKGRTQLALLPRALQCPSAAAPQAENGPAPAPAVATPPATEAPKMSNANFAKLF

Parental  LRK
          LRK
Retrocopy LRK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.00 RPM	19.46 RPM
SRP051959_heart	0.02 RPM	23.26 RPM
SRP051959_kidney	0.07 RPM	24.23 RPM
SRP051959_liver	0.02 RPM	15.03 RPM
SRP051959_lung	0.08 RPM	35.51 RPM
SRP051959_lymph_node	0.05 RPM	41.89 RPM
SRP051959_skeletal_muscle	0.02 RPM	24.02 RPM
SRP051959_spleen	0.08 RPM	32.02 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1695 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1695 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1695 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015330	1 retrocopy	retro_cjac_1695 ,