RetrogeneDB ID: retro_cjac_3281

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:20549763..20550766(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEIS2
• Ensembl ID: ENSCJAG00000020992
• Aliases: None
• Description: None

Sequence

>retro_cjac_3281
TACAATGAGCTGCCCCATTACAGCAGGATGAATGGAGTAGGGGTTCCCACTTCCATGTACAGAGACCCTCACCCACTGTG
GCCAATCCCCCCAGTTCACCACCTGAACCACAGGCTTCTGCTCCATGCCACACAGCACACCCCACACCCCAATGTCATGC
TGGCCAGCATGGGATCCACTGTCAACACCTTGAGGCAGGACAAGGACACGATCTATGGGCACCTGTTGTTTCCTCTGTTA
GCTCTGGTCTTTGAGAAGTGTGAGCTGGCAACCTGCACTCCCCAGGAACCTGGAGTGGCCGGCGGGAATGTCTGCTCCTC
TGACTCCTCCAACAAGGACATCACAGTCTTCGCCAAGCAGGTTCGTGCCGAAAAGCCACTTTTCTCCTCAAATCCAGAGG
TGGGCAATTTGATGATACAAGCAATACAAGTACTAAGGTTTCATCTTTTGGAATTAGGAAAGGTTCATGAACTGTGCAAT
AACTTCTGCCACCAATACATTAGCTGCTTGAAGGGGAAAATGTCCATCAACCTTATCACTGAAGAAAGAGATAGCAGTAC
CAAGTCAGATCATGAAGAACTTTCAGACTCCTCCACAAATCTCACTGACATAACCCTTCTTCTTGGTGAGACCACAATGA
TGCAACCTCAACCCACTCAGCAGGCACCTCAGGGCCCTCCAGTGGGGGTCATGCCTCCCAGAGCTGAGACAACAGCAGTG
AGCAAGGGGATGGTTTAGACAACAGTGTAGCTTCACCTGGTACAGATGACAATGATGATACAGATAAAGACAAAAAGCAC
CAGAAGATAAGAGGCATTCTCCCCAAAGTAGCAATAAATATCATGAGAGCATGGCTCTTCCAGCATCTCACACATCCGTA
CCCTTCCGAAGTGCAGAAGAAGCAGTGCAATACACAGGACTTCCAATACTCCAAGTAAACAACTGGTTTATTAATGCCAA
AAGAAGAACAGCACAGCCCATGATTGACCAGTCAAATCGAGCA

Alignment

ORF - retro_cjac_3281 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.17 %
• Parental protein coverage: 85.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YDELPHYGGMDGVGVPASMYGDPHAPRPIPPVHHLNHGPPLHATQHYGAHAPHPNVMPASMGSAVNDALK
          Y.ELPHY..M.GVGVP.SMY.DPH...PIPPVHHLNH...LHATQ....H.PHPNVM.ASMGS.VN..L.
Retrocopy YNELPHYSRMNGVGVPTSMYRDPHPLWPIPPVHHLNHRLLLHATQ----HTPHPNVMLASMGSTVN-TLR

Parental  RDKDAIYGHPLFPLLALVFEKCELATCTPREPGVAGGDVCSSDSFNEDIAVFAKQVRAEKPLFSSNPELD
          .DKD.IYGH.LFPLLALVFEKCELATCTP.EPGVAGG.VCSSDS.N.DI.VFAKQVRAEKPLFSSNPE..
Retrocopy QDKDTIYGHLLFPLLALVFEKCELATCTPQEPGVAGGNVCSSDSSNKDITVFAKQVRAEKPLFSSNPEVG

Parental  NLMIQAIQVLRFHLLELEKVHELCDNFCHRYISCLKGKMPIDLVIDERDGSSKSDHEELSGSSTNLAD-H
          NLMIQAIQVLRFHLLEL.KVHELC.NFCH.YISCLKGKM.I.L...ERD.S.KSDHEELS.SSTNL.D.H
Retrocopy NLMIQAIQVLRFHLLELGKVHELCNNFCHQYISCLKGKMSINLITEERDSSTKSDHEELSDSSTNLTD<H

Parental  NPSSWRDHDDATSTHSAGTPGPSSGGHASQSGDNSSEQGDGLDNSVASPGTGDDDDPDKDKKRQKKRGIF
          NPSSW.DH.DATSTHSAGT.GPSSGGHASQS.DNSSEQGDGLDNSVASPGT.D.DD.DKDKK.QK.RGI.
Retrocopy NPSSW*DHNDATSTHSAGTSGPSSGGHASQS*DNSSEQGDGLDNSVASPGTDDNDDTDKDKKHQKIRGIL

Parental  PKVATNIMRAWLFQHLTHPYPSEEQKK-QLAQDTGLTILQVNNWFINARRRIVQPMIDQSNRA
          PKVA.NIMRAWLFQHLTHPYPS.E..K....Q.TGL.ILQVNNWFINA.RR..QPMIDQSNRA
Retrocopy PKVAINIMRAWLFQHLTHPYPS-EVQK<EAVQYTGLPILQVNNWFINAKRRTAQPMIDQSNRA

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	8.10 RPM
SRP051959_heart	0.00 RPM	30.03 RPM
SRP051959_kidney	0.00 RPM	12.60 RPM
SRP051959_liver	0.00 RPM	3.12 RPM
SRP051959_lung	0.02 RPM	13.71 RPM
SRP051959_lymph_node	0.00 RPM	7.12 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.94 RPM
SRP051959_spleen	0.00 RPM	10.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3281 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3281 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3281 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020992	1 retrocopy	retro_cjac_3281 ,