RetrogeneDB ID: retro_cjac_963

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:31937821..31940094(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTNNA1
• Ensembl ID: ENSCJAG00000006820
• Aliases: None
• Description: None

Sequence

>retro_cjac_963
GTTCATGCAGGCAATGTAAACGTCAAGTGGGACCCCAAAGGTCTAGAGATCAGGACTCTGGCAGTTGAGAGACTGTTGGA
GTACCTTGTTACACAGGTTACAACCCTGGTAAACATCAATAGTAAGGGGCCCTCTAGTAAGAAGACAGGTTTTTCCAAGA
AGGCCCAGGTTTTGGCTGCATCTGTTGAACAAGCAACTGAGAATTTCTTAGACAAGGGGGATAAAATTGTGAAGAAGAAC
CAGTTTCTCAAGGAGGAGCTTGTGGCTGCTGTAGAAGATGTTCGAAAACAAGGGGATTTGATGAAGACTGCTGCGGGAGA
GTTCAGAGATGATCCCTGCTCTTCTGTGAAGCAAGGCAACATGGTTCGGGCAGCTCGAGCTTTGCTCTGTGCTGTTACCC
AGTTGCTGATTTTGGCTGACATGGCAGATGTCTACAAATTACTTGTTCAGCTCAAAGTTGTGGAAGATGGTATTTCGAAG
TTGAGGAATGCTGGCAATGAACAAGACTTAGGAATATAGTAAAAAGCCCTAAACCTGAAGTGGATAAGCTGAACATTATG
GCAGCCAAAGGGCAACAGGAACTGAAAGATGTTTGCCATCGTGATCAGATGGCTGCAGCTGGAAGAATCCTGCAGAAGAA
CATTCCGATCCTCTATACAGCATCCCAGGCATGCCTACAGCACCCTGATGTCACAGCCTATAAGGCCAACAGGGACCTGA
TATACAGGCAACTGCAGCAGGCGGTCACGGGCATTTCCAATGCAGCCCAGGCCACCGCCTCAGATGATGCTTCCCAGCAC
CAGCAGGGAGGAGGAGAACTGGCATATGCACTCAATAACTTTGAAAAACATATCATTGTAGTCCCCTTGAGCTTCAGTCA
GGAGCGCTTTAGGCCTTCCCTGGAGGAGCGCCTGGAAAGCATCATTAGTGGAGCTGCCTTGATGGCCGACTCATCCTGCA
CTCGTGATGATTGTTGTGAGTGAATTGTGGCAGAATGTAATGCTGTTTGCCAGGCCCTGCAGGACCTGCTTTTGGAGTAC
ATGGAAAATGCTGGGCGTAAAGAAAGAAGTGATGGACTCAGTTCTGCAATAGGTAAAATGACCAAGAAGACCAGGGACTT
GTGTAGACAGCTCCACAAAGCTGTCATGGACCATGTTTCAGATTATTTTCTGGAAACCAGTGTTCCACTTTTGGTATTGA
TTGAAGCTGCAAAGAATGGAAATGAGAAAGAAGTTAAGGAGTATGCCCAAGTTTTTGGTGGACATGCCAATAAATTGATT
GAGGTTGCCAACTTCGCCTGTTCCATCTCCAATAATGAAGAAGGTGTAAAGCTTGTTCGAATGTCTGCAAGCCAGTTAGA
AGCCCTCGGTCCTCAGGTTATCAACACTGCATTGGCTTTAGCAGCAAAACCACAGAGTAAACTGGCCCAAGAGAACATGG
ATCTTTTTAAAGAACAATGGGAAAAACAAGTCCCTGTTCTCACAGATGCCATTGATTACATAACTTCCACTGATGACTTC
TTGGCTGTCTCAGAGAATCACATTTTGGAAGATGTGAACAAATGTGTCATTGCTCTCCAAGAGAAGGATGTAGATGGCCT
GGACAGCACAGCTGGTGCAATTCCAGGCTGGGCAGCCCAGGTCGTTCACATAGTCACCTCAGAGATGGACTACTATGAGC
CAGGAGTCTACACAGAGAAGGTTCTGGAAGCCACTAAGCTGCTCTCTAACACAGTCATGCCACGTTTTACTGAGTAAGTA
GAAGCAGCCGTGGAAGCTCTTAGCTCGGACCCTGCCCAGCCCATGGATGAGAATGAGTTTATCGATGCCTCCTGCCTGGT
ATAGGATGGCATCTGGGACATCAGGAAAGCAGTGCTGATGATAAGGACCCCTGAGGAGTTGGATGACTCTGGCTTTGAGA
CTGAAGATTTCAATGTCAGAAGTAGGACGAGCGTCCAGACAGAAGATGATCAGCTGATAGCTGGCCAGAGTGCCTGGGTG
ATCATGGCTCAGCTTCCCCAGGAGCAGGAAGTGAAGACTGCAGAACAGGTGGCCAGCTTCCAGGAAGAAAAGAACAAGCT
GGATGCTGAAGTGTCCAAATGGGACAATAGTGGCAATGACATCATTGTGCTGGCCAAGCAGATGTGCATGATTATGACAG
AGATGTCTGACTTTACCTAAGGTAAAGGACCACTCAAAAATACATCAGATGTCATCAGTGCTGCCAAGAAAATTGCTGAG
ACAGGATCCAGGATGGAGAAGCTTGGCCACACC

Alignment

ORF - retro_cjac_963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.57 %
• Parental protein coverage: 83.33 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  INTGNINVKWDPKSLEIRTLAVERLLEPLVTQVTTLVNTNSKGPSNKKRGRSKKAHVLAASVEQATENFL
          ...GN.NVKWDPK.LEIRTLAVERLLE.LVTQVTTLVN.NSKGPS.KK.G.SKKA.VLAASVEQATENFL
Retrocopy VHAGNVNVKWDPKGLEIRTLAVERLLEYLVTQVTTLVNINSKGPSSKKTGFSKKAQVLAASVEQATENFL

Parental  DKGDKIAKESQFLKEELVAAVEDVRKQGDLMKTAAGEFADDPCSSVKRGNMVRAARALLSAVTRLLILAD
          DKGDKI.K..QFLKEELVAAVEDVRKQGDLMKTAAGEF.DDPCSSVK.GNMVRAARALL.AVT.LLILAD
Retrocopy DKGDKIVKKNQFLKEELVAAVEDVRKQGDLMKTAAGEFRDDPCSSVKQGNMVRAARALLCAVTQLLILAD

Parental  MADVYKLLVQLKVVEDGILKLRNAGNEQDLGMQYKAL-KPEVDKLNIMAAKRQQELKDVGHRDQMAAARG
          MADVYKLLVQLKVVEDGI.KLRNAGNEQDLG...KAL.KPEVDKLNIMAAK.QQELKDV.HRDQMAAA..
Retrocopy MADVYKLLVQLKVVEDGISKLRNAGNEQDLGI**KAL<KPEVDKLNIMAAKGQQELKDVCHRDQMAAAGR

Parental  ILQKNVPILYTASQACLQHPDVAAYKANRDLIYKQLQQAVTGISNAAQATASDDASQHQGGGGGELAYAL
          ILQKN.PILYTASQACLQHPDV.AYKANRDLIY.QLQQAVTGISNAAQATASDDASQHQ.GGG.ELAYAL
Retrocopy ILQKNIPILYTASQACLQHPDVTAYKANRDLIYRQLQQAVTGISNAAQATASDDASQHQQGGG-ELAYAL

Parental  NNFDKQIIVDPLSFSEERFRPSLEERLESIISGAALMADSSCTRDDRRERIVAECNAVRQALQDLLSEYM
          NNF.K.IIV.PLSFS.ERFRPSLEERLESIISGAALMADSSCTRDD..E.IVAECNAV.QALQDLL.EYM
Retrocopy NNFEKHIIVVPLSFSQERFRPSLEERLESIISGAALMADSSCTRDDCCE*IVAECNAVCQALQDLLLEYM

Parental  GNAGRKERSDALNSAIDKMTKKTRDLRRQQLRKAVMDHVSDSFLETNVPLLVLIEAAKNGNEKEVKEYAQ
          .NAGRKERSD.L.SAI.KMTKKTRDL.RQ.L.KAVMDHVSD.FLET.VPLLVLIEAAKNGNEKEVKEYAQ
Retrocopy ENAGRKERSDGLSSAIGKMTKKTRDLCRQ-LHKAVMDHVSDYFLETSVPLLVLIEAAKNGNEKEVKEYAQ

Parental  VFREHANKLIEVANLACSISNNEEGVKLVRMSASQLEALCPQVINAALALAAKPQSKLAQENMDLFKEQW
          VF..HANKLIEVAN.ACSISNNEEGVKLVRMSASQLEAL.PQVIN.ALALAAKPQSKLAQENMDLFKEQW
Retrocopy VFGGHANKLIEVANFACSISNNEEGVKLVRMSASQLEALGPQVINTALALAAKPQSKLAQENMDLFKEQW

Parental  EKQVRVLTDAVDDITSIDDFLAVSENHILEDVNKCVIALQEKDVDGLDRTAGAIRGRAARVIHVVTSEMD
          EKQV.VLTDA.D.ITS.DDFLAVSENHILEDVNKCVIALQEKDVDGLD.TAGAI.G.AA.V.H.VTSEMD
Retrocopy EKQVPVLTDAIDYITSTDDFLAVSENHILEDVNKCVIALQEKDVDGLDSTAGAIPGWAAQVVHIVTSEMD

Parental  NYEPGVYTEKVLEATKLLSNTVMPRFTEQVEAAVEALSTDPAQPMDENEFIDASRLAYDGIRDIRKAVLM
          .YEPGVYTEKVLEATKLLSNTVMPRFTE.VEAAVEALS.DPAQPMDENEFIDAS.L..DGI.DIRKAVLM
Retrocopy YYEPGVYTEKVLEATKLLSNTVMPRFTE*VEAAVEALSSDPAQPMDENEFIDASCLV*DGIWDIRKAVLM

Parental  IRTPEELDDSDFETEDFDVRSRTSVQTEDDQLIAGQSARAIMAQLPQEQKAKIAEQVASFQEEKSKLDAE
          IRTPEELDDS.FETEDF.VRSRTSVQTEDDQLIAGQSA..IMAQLPQEQ..K.AEQVASFQEEK.KLDAE
Retrocopy IRTPEELDDSGFETEDFNVRSRTSVQTEDDQLIAGQSAWVIMAQLPQEQEVKTAEQVASFQEEKNKLDAE

Parental  VSKWDDSGNDIIVLAKQMCMIMMEMTDFTRGKGPLKNTSDVISAAKKIAEAGSRMDKLGRT
          VSKWD.SGNDIIVLAKQMCMIM.EM.DFT.GKGPLKNTSDVISAAKKIAE.GSRM.KLG.T
Retrocopy VSKWDNSGNDIIVLAKQMCMIMTEMSDFT*GKGPLKNTSDVISAAKKIAETGSRMEKLGHT

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	0.16 RPM	222.76 RPM
SRP051959_heart	0.42 RPM	186.65 RPM
SRP051959_kidney	0.13 RPM	136.31 RPM
SRP051959_liver	0.06 RPM	70.57 RPM
SRP051959_lung	0.11 RPM	120.10 RPM
SRP051959_lymph_node	0.02 RPM	34.29 RPM
SRP051959_skeletal_muscle	0.09 RPM	31.86 RPM
SRP051959_spleen	0.11 RPM	96.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_963 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_963 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_963 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006820	1 retrocopy	retro_cjac_963 ,
Myotis lucifugus	ENSMLUG00000012995	1 retrocopy	retro_mluc_422,
Otolemur garnettii	ENSOGAG00000011865	1 retrocopy	retro_ogar_516,