RetrogeneDB ID: retro_cjac_4046

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:20743486..20744511(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000005119
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CBLL1
• Ensembl ID: ENSCJAG00000016379
• Aliases: None
• Description: None

Sequence

>retro_cjac_4046
GATAATGGGTTGCTAGGCACTCATACTTATGGATCCTTGGGTGGCCTTGATGTTAGCAGAAGAATTCATATAAAGGCCGT
TTTTGAGGAAGTAGACAAACCTAAATTTGTGTCTCAACTCCAAGGAATGTGAACAAGATGCCTGCTGGTGGACAAGAACG
TAAATATAATGAAGGGAAGTACTACTCTAAACGAGGTAAACTGTTAAGGAAAGAGAAAAAAATTCCTGGTTACCTTTGGG
GGGACATTAAGATGAACGTGATAGGTAAAAAGGATGATTTACCAATTCATTTCTGTGACAAATGTGATTTGCCTATTAAA
ATCTATGGGCGAATAATTCCATGCAAGCATGCTTTTTGCTATGACTGTGCTAATTTATATGACAAAAACGGATGTAAAAT
ATGTCCAGGCTGTAGTTATCCTGTGCGTCGAATTGAGAAGCATAAACGAGGTTCTCTCTTCACGTGTAGTGCCATTCACG
AATGCAAGAGAACATATTCATCTCAGAAAAGCTTACAGGCTCATATCAAACACTGCAATAAGAGAGCTGGAAAACATGTT
AGCTGCACTTCACTTGAAAAAGTTCGTCCCCGTATTGATCCGCCACAAACTGAAATCTCTGAAATCCCTAAAAGACTGCA
AGATGAGGGCCATCGAAGCTATATTCCACCAGAGCAGCACACCATGATGCCACCACCGACTGTGCCACATATGCTACACA
AGCACTATAATTGGCCACCTAAGGATATTCAGGCTCCCCCCAAAGAATTATCTCCAAGTCCGCCTTTTCCCATCCAGTGG
GAAACCGTTAGTATTTTTACAAGAAAAGATGGCAAGATAATAACTGAGCATATTCAGAAGTACTCCAATTCTGGTGCTAA
GAAACCATCACCTCCTGACTATTCTCCTGAGTATCAAGGTCAACCAGTGGTATCATACCCTGATCATAATATGCCTCGAA
AACAGCATTATGCACAACCTCTATCTCCATCATCAACGGTAAACCATCCAATGCCATATCCTCCT

Alignment

ORF - retro_cjac_4046 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.43 %
• Parental protein coverage: 70.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DNELQGTNSSGSLGGLDVRRRIPIKLISKQANKAKPAPRTQ-RTINRMPAKAPPGDEEGFDYNEEERYDC
          DN.L.GT...GSLGGLDV.RRI.IK.......K.K.....Q.R..N.M....P.G..E...YNE...Y..
Retrocopy DNGLLGTHTYGSLGGLDVSRRIHIKAVFEEVDKPKFVSQLQ<RNVNKM----PAGGQER-KYNEGKYYS-

Parental  KGGELFGNQRRFPGHLFWDFQINILGEKDDTPVHFCDKCGLPIKIYGRMIPCKHVFCYDCAILHEKKGDK
          K.G.L.......PG.L..D...N..G.KDD.P.HFCDKC.LPIKIYGR.IPCKH.FCYDCA.L..K.G.K
Retrocopy KRGKLLRKEKKIPGYLWGDIKMNVIGKKDDLPIHFCDKCDLPIKIYGRIIPCKHAFCYDCANLYDKNGCK

Parental  MCPGCSDPVQRIEQCTRGSLFMCSIVQGCKRTYLSQRDLQAHINHRHMRAGKPVTRASLENVHPPIAPPP
          .CPGCS.PV.RIE...RGSLF.CS....CKRTY.SQ..LQAHI.H...RAGK.V...SLE.V.P.I.PP.
Retrocopy ICPGCSYPVRRIEKHKRGSLFTCSAIHECKRTYSSQKSLQAHIKHCNKRAGKHVSCTSLEKVRPRIDPPQ

Parental  TEIPDRFIMPPDKHHMSHIPPKQHIMMPPPPLQHVPHEHYNQPHEDIRAPPAELSMAPPPPRSVSQETFR
          TEI........D..H.S.IPP.QH.MMPPP...H..H.HYN.P..DI.APP.ELS..P.PP.....ET..
Retrocopy TEISEIPKRLQDEGHRSYIPPEQHTMMPPPTVPHMLHKHYNWPPKDIQAPPKELS--PSPPFPIQWETVS

Parental  ISTRKHSNLITVPIQDDSNSGAREPPPPAPAPAHHHPEYQGQPVVSHP---HHIMP--PQQHYAPPPPPP
          I.TRK....IT..IQ..SNSGA..P.PP...P..........P....P...H...P..P......P.P.P
Retrocopy IFTRKDGKIITEHIQKYSNSGAKKPSPPDYSPEYQGQPVVSYPDHNMPRKQHYAQPLSPSSTVNHPMPYP

Parental  P
          P
Retrocopy P

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	12.36 RPM
SRP051959_heart	0.00 RPM	9.86 RPM
SRP051959_kidney	0.02 RPM	8.96 RPM
SRP051959_liver	0.00 RPM	5.35 RPM
SRP051959_lung	0.00 RPM	10.20 RPM
SRP051959_lymph_node	0.00 RPM	8.97 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.48 RPM
SRP051959_spleen	0.02 RPM	10.40 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4046 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4046 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4046 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016379	1 retrocopy	retro_cjac_4046 ,
Homo sapiens	ENSG00000105879	1 retrocopy	retro_hsap_49,
Gorilla gorilla	ENSGGOG00000004921	1 retrocopy	retro_ggor_164,
Microcebus murinus	ENSMICG00000012936	1 retrocopy	retro_mmur_1635,
Nomascus leucogenys	ENSNLEG00000008660	1 retrocopy	retro_nleu_19,
Pongo abelii	ENSPPYG00000017904	1 retrocopy	retro_pabe_112,
Pan troglodytes	ENSPTRG00000019583	1 retrocopy	retro_ptro_67,
Rattus norvegicus	ENSRNOG00000007253	1 retrocopy	retro_rnor_1063,