RetrogeneDB ID: retro_cjac_1889

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:18934422..18935876(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPAA1
• Ensembl ID: ENSCJAG00000021455
• Aliases: None
• Description: None

Sequence

>retro_cjac_1889
GCCAGCTCCAAGTCGCTTGTGCTCACCGTGCCCTGTGGCTCTGACTCTACCAACACTCAGGCTGTGGGGCTGCTGCTGGC
ACTGGCTGCCCACTTCTGGGAACAGATCTCCTAAGCCAAAGATACCATGTTCCTGGTAACAGAACATGACCTTCTGGGCA
CTGAGGCTTGGCTTGAAGCCTACCATGATGTAAATGTCACAGGCATGCAGTCATCCCCCCTGCAGGGCTGAGCTGGGACC
ATTCAGGCCACCGTGACCCTGGAGCTGAGCAGTGATGTGGTCACTAGCCTGGGGCTGTGAAGGGGTTCAACAGGCAGCTG
CCCAATCTAGACCTGCTCAATCTCTTCCAGACCTTCTGCGAGAAAGGGAACCTGCTGTGCATGCTTCAGGGCAAGCTACA
GCCCCAGGACTATACATTGTCATTGGACACACCACTGCAATGCCTGCAGATACTGCTGCTCATGGTTCCGGAGCAGGACT
CCGGCCGCCCCCACGGCTCCCATGGCCTCTTCCAGTGCTGCTGTGTGGAGGCCCTAACCCTGCGTGGCATCAGTAGCTTC
CGCCAGTACAAGTATGACCTGGTGGCAGTGGTCAAAGCTTTGGAGGGCATGCTCCGAAACTCAACCACCTCCTGGAGCGC
CTGCACCAGTCCTTCTTCCTCTACCTGCTCACACCCTCTCCCGGTTAGTTTCGGTTGGCCCCTAAGTGCCTGCCACCAGC
TTCTTGCTCCTGTCCTTGGTCTCAAGGTGCTGGAACTATGGATGCAGCTGCATGAGGCTGGAGTGGGCCTTGAGAAGCCC
TGGGGAAGGGGGCTGGCTCTGGCCCCAGTGTCCCCCTTCCCCCAGCACAGGGTGTGGGGCTGGCCTCGTTCGTGGCACCT
CTGATGATCTCACAGGCCATGGGACTGGCTTTCGATGTCCTGCCAGTGCTGGGCCAACAAGTGGCCACCCAGCACTTCCC
AGTGGCAGAGGCTGAGGTTGTAGTGCTGACACTGCTGGTGATTTACGCAGCTGGCCTGGCCCAGCCCCACACAACCCATC
AGGTGGTAAAAACACAGGCCCCAGGCAGGGGCTGGATGGCGCTGAAGCTAGTAGCTCTGCTCTACCTAACACTGCAGCTG
GGCTGCATTGCCCTCACCAACGTCTCACTGGGCTTCCTGCTGGACACCACTATGGGCAGTGCTGCTGCCCTAGCCGAGCC
TCATGGGCTACAGACCCTCTATGCTGCCTTTCTAGTGCTGACTAGCCCGGGCAGCCATGCTTTTTGGCAGCCTATTCCTG
TGGCAGGAACTGCAGGAGGTGGCACCGTCACTGGCTGCGAGCTGACAGCTCTTCCTGGCAGCACTGGCCCAGGGTGTGCT
GGAGCACCACACCTACGGTTCCCTGCTCTTCCCACTGCTGTCCCTGGGCCTCTACCCCTACTGGCTGCTTTTCTGGAATG
TGGTCTTCTGGAAG

Alignment

ORF - retro_cjac_1889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.09 %
• Parental protein coverage: 86.15 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  ASTESLVLTVPCGSDSTNSQAVGLLLALAAHFRGQIYWAKDIIFLVTEYDLLGTEAWLEAYHDVNVTGMQ
          AS..SLVLTVPCGSDSTN.QAVGLLLALAAHF..QI..AKD..FLVTE.DLLGTEAWLEAYHDVNVTGMQ
Retrocopy ASSKSLVLTVPCGSDSTNTQAVGLLLALAAHFWEQIS*AKDTMFLVTEHDLLGTEAWLEAYHDVNVTGMQ

Parental  SSPLQGRAGAIQAAVALELSSDMVTSLDVAVEGLNGQLP-NLDLLNLFQTFCQKGGLLCTLQGKLQPQDW
          SSPLQG.AG.IQA.V.LELSSD.VTSL.....G..G..P.NLDLLNLFQTFC.KG.LLC.LQGKLQPQD.
Retrocopy SSPLQG*AGTIQATVTLELSSDVVTSLGL-*RGSTGSCP<NLDLLNLFQTFCEKGNLLCMLQGKLQPQDY

Parental  T-SLDGPLQGLQMLLLMVLRQASGRPHGSHGLFLRYRVEALTLRGINSFRQYKYDLVAVGKALEGMFR-K
          T.SLD.PLQ.LQ.LLLMV..Q.SGRPHGSHGLF....VEALTLRGI.SFRQYKYDLVAV.KALEGM.R.K
Retrocopy TLSLDTPLQCLQILLLMVPEQDSGRPHGSHGLFQCCCVEALTLRGISSFRQYKYDLVAVVKALEGMLR<K

Parental  LNHLLERLHQSFFLYLLP-ALSRFVSIGLYMPAAGFLLL-VLGLKALELWMQLHEAGVGLEEPRGSPGPS
          LNHLLERLHQSFFLYLL...LSR.VS.G...PA..FLLL.VLGLK.LELWMQLHEAGVGLE.P.G.....
Retrocopy LNHLLERLHQSFFLYLLT<TLSRLVSVGP*VPATSFLLL<VLGLKVLELWMQLHEAGVGLEKPWGRGLAL

Parental  AQVMAPP-SQGVG-LASLVAPLLISQAMGLALYVLPVLGQHVAAQHFPVAEAEAVVLTLLAIYAAGLALP
          A.V...P.S.G.G.LAS.VAPL.ISQAMGLA..VLPVLGQ.VA.QHFPVAEAE.VVLTLL.IYAAGLA.P
Retrocopy APVSPFP>STGCG>LASFVAPLMISQAMGLAFDVLPVLGQQVATQHFPVAEAEVVVLTLLVIYAAGLAQP

Parental  HNTHRVVSTQAPDRGWMALKLVALIYLALQLGCIALTNFSLGFLLAATMVPTAALAKPHGSRTLYAALLV
          H.TH.VV.TQAP.RGWMALKLVAL.YL.LQLGCIALTN.SLGFLL..TM...AALA.PHG..TLYAA.LV
Retrocopy HTTHQVVKTQAPGRGWMALKLVALLYLTLQLGCIALTNVSLGFLLDTTMGSAAALAEPHGLQTLYAAFLV

Parental  LTSP-AATLFGSLFLWRELQEAPLSLAEGWQLFLAALAQGVLEHHTYGALLFPLLSLGLYPCWLLFWNVL
          LTSP.AA.LFGSLFLW.ELQE...SLA...QLFLAALAQGVLEHHTYG.LLFPLLSLGLYP.WLLFWNV.
Retrocopy LTSP>AAMLFGSLFLWQELQEVAPSLAAS*QLFLAALAQGVLEHHTYGSLLFPLLSLGLYPYWLLFWNVV

Parental  FWK
          FWK
Retrocopy FWK

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	13.67 RPM
SRP051959_heart	0.00 RPM	20.36 RPM
SRP051959_kidney	0.00 RPM	28.95 RPM
SRP051959_liver	0.00 RPM	25.26 RPM
SRP051959_lung	0.00 RPM	19.00 RPM
SRP051959_lymph_node	0.00 RPM	21.92 RPM
SRP051959_skeletal_muscle	0.00 RPM	24.31 RPM
SRP051959_spleen	0.00 RPM	20.32 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1889 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1889 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1889 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021455	1 retrocopy	retro_cjac_1889 ,
Dipodomys ordii	ENSDORG00000008463	1 retrocopy	retro_dord_298,