RetrogeneDB ID: retro_cjac_2503

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:18322973..18324019(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021364
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: STRAP
• Ensembl ID: ENSCJAG00000021593
• Aliases: None
• Description: None

Sequence

>retro_cjac_2503
ATGGCAATGAGACAGATGCCGCTCACCTGCTCTGGCCACACGCGGCCCGTAGTTGATTTGGCCTTCAGTGGCATCACGCC
TTATGAGTATTTCTTAATCAGCGCTTGCAAAGATGGTAAACCTATGCTACGCCAGGGAGATACAGGAGACTGGATTGGAA
CATTTTTGGGTCATAAAGGTGCTGTTTGGGTGGCAACACTGAATAAGGATGCCATCAAAGCGGCTACAGCAGCTGCAGAT
TTCACAGCCAGAGTGTGGGATGCTGTCTCGGGAGATGAATTGATGACCCTGGCTCATAAACACATTGTCAAAACTGTGGA
TTTCACACAGGATAGTAATTATTTGTTAAGAGGGGGACAGGATAAACTGTTACCCATCTATGACTTGAACAAACCTGAAG
CAGAACCTAAGGAAATTAGTGGTCACACTTGTGGTATAAAAAAAAGCTCTGTGGTTCAGTGAAGATAAACAGATTCTTTC
TGCTGATGACAAAACCGTTCGACTTTGGGATCATGCTACTATGACAGAAGTGAAATCTCTCAATTTTAATATGTCTGTTA
GTAGTATGGAATATATTCCCGAGGGAGAGATTTGGGTTATAACTTATGGACGATCTATTGCTTTTCATAGTGCAGTAAGT
TTGGACCCAATTAAATTCTTTGAAGCTCCTGCAACCATCAATTCTGCCTCTCTTCATCCTGAGAAGGAATTTATTGTTGC
AGGTGAAGAAGATTTTAAACTTTATACGTATGATTATAACAGTGGAGAAGAATTAGAATCCTACAAGGGACACTTTGGTC
CTATTCACTGTGTGAGATTTAGTCCTGGTGGGGAACTCTATGCCAGTGGTTCCGAAGATGGAACATTGAGAATATGGCAA
ACTGTGGTAGGAAAAACATATGGCCTTTGGAAATGTGTGCTTCCTGAAGAAGATAGTGGTGAGCAGGCAAAGCCAAAGAT
TGGTTTCAGAGACAACAGAGGAACTAGAAAAAATTGCGTCAGAGAATTCAGATTGCATCTATTCTTCAACTCCTGATGTT
AAGGCC

Alignment

ORF - retro_cjac_2503 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.48 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAMRQTPLTCSGHTRPVVDLAFSGITPYGYFLISACKDGKPMLRQGDTGDWIGTFLGHKGAVWGATLNKD
          MAMRQ.PLTCSGHTRPVVDLAFSGITPY.YFLISACKDGKPMLRQGDTGDWIGTFLGHKGAVW.ATLNKD
Retrocopy MAMRQMPLTCSGHTRPVVDLAFSGITPYEYFLISACKDGKPMLRQGDTGDWIGTFLGHKGAVWVATLNKD

Parental  ASKAATAAADFTAKVWDAVSGDELMTLAHKHIVKTVDFTQDSNYLLTGGQDKLLRIYDLNKPEAEPKEIS
          A.KAATAAADFTA.VWDAVSGDELMTLAHKHIVKTVDFTQDSNYLL.GGQDKLL.IYDLNKPEAEPKEIS
Retrocopy AIKAATAAADFTARVWDAVSGDELMTLAHKHIVKTVDFTQDSNYLLRGGQDKLLPIYDLNKPEAEPKEIS

Parental  GHTSGIKK-ALWCSEDKQILSADDKTVRLWDHATMTEVKSLNFNMSVSSMEYIPEGEILVITYGRSIAFH
          GHT.GIKK.ALW.SEDKQILSADDKTVRLWDHATMTEVKSLNFNMSVSSMEYIPEGEI.VITYGRSIAFH
Retrocopy GHTCGIKK>ALWFSEDKQILSADDKTVRLWDHATMTEVKSLNFNMSVSSMEYIPEGEIWVITYGRSIAFH

Parental  SAVSLDPIKSFEAPATINSASLHPEKEFLVAGGEDFKLYKYDYNSGEELESYKGHFGPIHCVRFSPDGEL
          SAVSLDPIK.FEAPATINSASLHPEKEF.VAG.EDFKLY.YDYNSGEELESYKGHFGPIHCVRFSP.GEL
Retrocopy SAVSLDPIKFFEAPATINSASLHPEKEFIVAGEEDFKLYTYDYNSGEELESYKGHFGPIHCVRFSPGGEL

Parental  YASGSEDGTLRLWQTVVGKTYGLWKCVLPEEDSAELAKPKLGFPE-TTEEELEEMTSENSDCIYSSTPDV
          YASGSEDGTLR.WQTVVGKTYGLWKCVLPEEDS.E.AKPK.GF...T.E.E.....SENSDCIYSSTPDV
Retrocopy YASGSEDGTLRIWQTVVGKTYGLWKCVLPEEDSGEQAKPKIGFRD>TEELE--KIASENSDCIYSSTPDV

Parental  KA
          KA
Retrocopy KA

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	17.71 RPM
SRP051959_heart	0.14 RPM	16.17 RPM
SRP051959_kidney	3.17 RPM	20.83 RPM
SRP051959_liver	0.32 RPM	27.94 RPM
SRP051959_lung	0.20 RPM	17.37 RPM
SRP051959_lymph_node	0.21 RPM	14.09 RPM
SRP051959_skeletal_muscle	0.02 RPM	23.93 RPM
SRP051959_spleen	0.02 RPM	17.42 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2503 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2503 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2503 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007422	2 retrocopies	retro_chof_1098, retro_chof_1620,
Callithrix jacchus	ENSCJAG00000006810	1 retrocopy	retro_cjac_3104,
Callithrix jacchus	ENSCJAG00000021593	1 retrocopy	retro_cjac_2503 ,
Homo sapiens	ENSG00000023734	2 retrocopies	retro_hsap_2092, retro_hsap_3723,
Gorilla gorilla	ENSGGOG00000009939	1 retrocopy	retro_ggor_1633,
Macaca mulatta	ENSMMUG00000013307	2 retrocopies	retro_mmul_1695, retro_mmul_985,
Mus musculus	ENSMUSG00000030224	1 retrocopy	retro_mmus_794,
Nomascus leucogenys	ENSNLEG00000004160	2 retrocopies	retro_nleu_1301, retro_nleu_1970,
Ochotona princeps	ENSOPRG00000015211	3 retrocopies	retro_opri_1029, retro_opri_217, retro_opri_541,
Pongo abelii	ENSPPYG00000004334	3 retrocopies	retro_pabe_2005, retro_pabe_3134, retro_pabe_3212,
Pan troglodytes	ENSPTRG00000004734	2 retrocopies	retro_ptro_1538, retro_ptro_2616,
Tursiops truncatus	ENSTTRG00000003466	2 retrocopies	retro_ttru_581, retro_ttru_974,