RetrogeneDB ID: retro_cjac_1869

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:163865342..163866210(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC11
• Ensembl ID: ENSCJAG00000004928
• Aliases: None
• Description: None

Sequence

>retro_cjac_1869
AAGAAAGAGCTGGAGGAGAGCATGTCCTTGGGTCTGAATACCCAGGTCACCAGCATCCAGGTGCAAAGGCAGGTAGTGCA
GTAGCTGGAGGAAGAGGAGGTGCACCTTATAGAAAAACACAAAGCACAGATTAAACTTTAGAATGAACAGGATAAGCTGG
AGAAAGAGGAAGCAAAGCAGGAAATTGAAACCTTTTTGCAAAAAGTCTTCCAGGAGAAGGTGGAACATATTTGACAGAAA
TACAGAAAAGAAGGACTTGAACATAAGCTTTGTGCAAGGGTCCTTCAAGACTTACAGGAAGAGGCTGATTAAAAAAGCAA
CAAAGAGAAGACATGAGAAGGAAACAGAAGACATCTCATAAAATATGCAGCATAGCAACATCAGGGGAATAAAGCTTTGG
AGAAATTATTAGACAAAATAATAGAGGCAGAGAAGGAAAAAAAAATGTTGGCCAAGAAGGACAGGAAGTAAGATTGGAAA
AGGAGGCAAGGAAACAATTTGTGAATGAGGTTATGTGTACAGGAAAAGTTCAAGTTCAAGAAATATTGCAAAGAAAAGCA
AAAGAACAGAAAAGATATGCTGTGGAACAGGATTACATAAATGAAGGTTTTAAAGAAGTTAAGGATGAAGAGGAAAATGT
TGCAAGATGCAGTGGTTTAGCTTAGCAATATAAGAGACAATTGCAAAAGCGAATCTTCCACCAGCAGCAGGCCCGGGAAG
CAGAGAAGAAAGAGGAACAAAGAGTGTTTGAAGCAGGGATAACAGCAAACAAGATTTGCCAGGACAGAATTCAGGAGACA
CCAACCACCATCAAATGCCATCCAGAAATAGGCATTTTATGTGGTAACTATGCCCTAATAGGCTTCCA

Alignment

ORF - retro_cjac_1869 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.43 %
• Parental protein coverage: 56.61 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QKELMENTRLGLNAQITSIKAQRKAEQLLKEEEARLVESNNAQIKHENEQDKLKKQKAKQETRTILQKTL
          .KEL.E...LGLN.Q.TSI..QR...Q.L.EEE..L.E...AQIK..NEQDKL.K..AKQE..T.LQK..
Retrocopy KKELEESMSLGLNTQVTSIQVQRQVVQ*LEEEEVHLIEKHKAQIKL*NEQDKLEKEEAKQEIETFLQKVF

Parental  QERIEHIQQEYREEQDLNMKLVQRALQDLQEEAD-KKKQKREDMIREQKIYR-KYLAQRREEEKAQEKEF
          QE..EHI.Q.YR.E..L..KL..R.LQDLQEEAD..KKQ.REDM.R.QK....KY.A......KA.EK..
Retrocopy QEKVEHI*QKYRKE-GLEHKLCARVLQDLQEEAD<LKKQQREDMRRKQKTSH>KYAA*QHQGNKALEKLL

Parental  DRILEEDKEKK-LAEKDK-ELKLEKEARKQLVDEVMCTRKLQVQEKLQREAKEQEERAKEQKHINEGLKE
          D.I.E..KEKK.LA.KD..E..LEKEARKQ.V.EVMCT.K.QVQE.LQR.AKEQ...A.EQ..INEG.KE
Retrocopy DKIIEAEKEKKMLAKKDR<EVRLEKEARKQFVNEVMCTGKVQVQEILQRKAKEQKRYAVEQDYINEGFKE

Parental  LNCEEKENFARRQRLAQEYRKQLQMQIAYQQQSQEAEKEEKRREFEAGIAANKICLDKIQEILST-QQVL
          ....E.EN.AR...LA..Y..QLQ..I..QQQ..EAEK.E..R.FEAGI.ANKIC.D.IQE...T..Q..
Retrocopy VK-DEEENVARCSGLA*QYKRQLQKRIFHQQQAREAEKKEEQRVFEAGITANKICQDRIQETPTT<HQMP

Parental  PQNIHPMRKACPRELP
          ..N.H.M...CP..LP
Retrocopy SRNRHFMW*LCPNRLP

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	0.07 RPM
SRP051959_heart	0.00 RPM	0.05 RPM
SRP051959_kidney	0.00 RPM	1.18 RPM
SRP051959_liver	0.00 RPM	0.04 RPM
SRP051959_lung	0.00 RPM	4.16 RPM
SRP051959_lymph_node	0.00 RPM	0.09 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.37 RPM
SRP051959_spleen	0.00 RPM	0.15 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1869 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1869 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1869 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_566

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002660	1 retrocopy	retro_btau_906,
Callithrix jacchus	ENSCJAG00000004928	1 retrocopy	retro_cjac_1869 ,
Equus caballus	ENSECAG00000010219	1 retrocopy	retro_ecab_566,