RetrogeneDB ID: retro_cjac_3199

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:25232362..25233460(+)
• Located in intron of: ENSCJAG00000013099

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000009625
• Aliases: None
• Description: None

Sequence

>retro_cjac_3199
AAGGAGCACCTAGAACCTAGGACCATGTTGTGTGACAGGTGGACAGAGAAGTCACCCTGCCCCAGGAAGCAGGTGCTTGG
CCACTCAGAGTTCCTCAGCAGGAAGAAGAAAAAGAAGTCACCTCTGGCATGTTCCGTGGTTGTGGAGTGAAAAACCTCCC
CAGATCCCAGACACAGCGAGGAGAAGACCAGAGTTTGCAAGAAGCTCAAAAAACACCAGAGGAAAAAAGAGGGGCTCAGT
ACACCACAGCCTTCTCAGTCTAGGACCCTTGATTCTGCAAGGAAAGGGATGCTGCCTGCATTTGCTCAGTGGAGAAGGAA
GGACAAGTAGGAAGCCTTGGGGTAGAATGGAAGCAGGGAAGGCCCGGGGAACACAGCGGGAAAGTAAAGAAGACAAAAAA
ATCCATCAGAAGGGAGACACTCTCCCATGCCACACTCCATGGTCCAGGTCCATGAAGAGTAGCCCTAGGAAACGAAGTAA
AAAGAAGCCAGTCGAAATTGAGGCTCCAAAACACATCGCAATATGAGATGGCCCTAAGTTCCCAGCAAAGAATAAACTGA
GGTCCAAGAAAAACATAGAGCAGCGAAGTCACTGAGGATGTGGCTCTGAAAAGGAAAAAAAGAAAAGAAAAGAGAGTGGG
GTAGAAGGAAACCCATGGAAAGAGAAAACAGACACAGACACAGAGATGATGCTGGAAAAGAATGGCAACATGGACAAGGG
CACACTGAACAGGTGAGGCAAAAGGCCTTGCAACAGACTGATCTTAAGTTCGGCAAAACAGAAGCTTCTAAAACCAGAAA
GTGGACAGTAACCCAGTCTGGCCAGTGGGATACTGCTGGCTTTAAGAACAAGGATCAATAACATAAATTTCTCAAACCTG
GGTGGCTTGAAAAATCTGACCCTTCATTTAGCTGCCCCCCTGGCATGACTGCAAAGCCGAACATGACCCTAAGCAAGAAG
GCAGCAAATAGCCTGCAGCAGAACCTGCAGCAGGATTACAACTAGGACATAAGCTGGAAGTTCAACCTAGGAGCAAGCTT
TGGCTTCTCCACTGCCTCAAACAAAATCTTTTATATTGGTAGGAATGCTTCCAAGTCA

Alignment

ORF - retro_cjac_3199 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.52 %
• Parental protein coverage: 81.06 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  EEQVESETMLRARRTEKSCSPRKQVLGHLEFVSREKKKKKSPLAMSHASGLKTSPDPRQGKEETRFGKKL
          .E..E..TML..R.TEKS..PRKQVLGH.EF.SR.KKKKKSPLA.S.....KTSPDPR...E.TR..KKL
Retrocopy KEHLEPRTMLCDRWTEKSPCPRKQVLGHSEFLSR-KKKKKSPLACSVVVE*KTSPDPRHSEEKTRVCKKL

Parental  KKHKK-EKKGAQDPT---VQDPWVCEAGDAGDTCSVGKEGEEQAAVGQKRKQKSPREHSEKVKK-EKKVH
          KKH...EK.GAQ..T...V.DP..C...DA...CSV.KEG......G...KQ..P.EHS.KVKK..KK.H
Retrocopy KKHQR<EKRGAQYTTAFSV*DP*FCKERDAACICSVEKEGQV-GSLGVEWKQGRPGEHSGKVKK<DKKIH

Parental  QEGEALPGHSQPPRSMESSPRKGRKKKPVKVEAPEYIPIGDGPKAPVKKKMKSKKKAEH-PVIEEPALKR
          Q.G..LP.H....RSM.SSPRK..KKKPV..EAP..I.I.DGPK.P.K.K..SKK..E...V.E..ALKR
Retrocopy QKGDTLPCHTPWSRSMKSSPRKRSKKKPVEIEAPKHIAI*DGPKFPAKNKLRSKKNIEQ>EVTEDVALKR

Parental  KK-KKSTESGVAGDPGKEDADTDLEVVLEKKGNMD-EAHIDQVRRKALQEEIDRESGKTEASETRKLMGT
          KK.KK..ESGV.G.P.KE..DTD.E..LEK.GNMD...H..QVR.KALQ...D...GKTEAS.TRK...T
Retrocopy KK<KKRKESGVEGNPWKEKTDTDTEMMLEKNGNMD<QGHTEQVRQKALQQT-DLKFGKTEASKTRKWTVT

Parental  QFGQWDTASFENEEQ-KLKFLKLMGGFKNLST-SFSRPPSTTARPNMALSKKAADSLQQNLQRDYDRAMS
          Q.GQWDTA.F.N..Q....F..L.GG.KNL...SFS.PP..TA.PNM.LSKKAA.SLQQNLQ.DY....S
Retrocopy QSGQWDTAGFKNKDQ>NINFSNL-GGLKNLTL<SFSCPPGMTAKPNMTLSKKAANSLQQNLQQDYN*DIS

Parental  WKYSRGAGLGFSTAPNKIFYIDRNASRS
          WK...GA..GFSTA.NKIFYI.RNAS.S
Retrocopy WKFNLGASFGFSTASNKIFYIGRNASKS

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	1.11 RPM	5.88 RPM
SRP051959_heart	0.70 RPM	8.51 RPM
SRP051959_kidney	0.82 RPM	12.02 RPM
SRP051959_liver	0.19 RPM	6.87 RPM
SRP051959_lung	1.33 RPM	7.29 RPM
SRP051959_lymph_node	2.10 RPM	7.03 RPM
SRP051959_skeletal_muscle	0.98 RPM	9.13 RPM
SRP051959_spleen	0.92 RPM	7.98 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3199 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3199 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3199 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_920

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018032	2 retrocopies	retro_cfam_1557, retro_cfam_1763,
Callithrix jacchus	ENSCJAG00000009625	1 retrocopy	retro_cjac_3199 ,
Homo sapiens	ENSG00000103550	3 retrocopies	retro_hsap_3487, retro_hsap_4007, retro_hsap_979,
Gorilla gorilla	ENSGGOG00000005673	1 retrocopy	retro_ggor_2691,
Macaca mulatta	ENSMMUG00000002707	2 retrocopies	retro_mmul_1771, retro_mmul_798,
Nomascus leucogenys	ENSNLEG00000012496	2 retrocopies	retro_nleu_1618, retro_nleu_551,
Otolemur garnettii	ENSOGAG00000010065	4 retrocopies	retro_ogar_1115, retro_ogar_1480, retro_ogar_1481, retro_ogar_2259,
Pongo abelii	ENSPPYG00000007151	3 retrocopies	retro_pabe_3293, retro_pabe_828, retro_pabe_920,
Pan troglodytes	ENSPTRG00000007836	3 retrocopies	retro_ptro_2360, retro_ptro_767, retro_ptro_924,