RetrogeneDB ID: retro_cjac_2288

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:148768326..148769103(-)
• Located in intron of: ENSCJAG00000019226

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP1B1
• Ensembl ID: ENSCJAG00000010317
• Aliases: None
• Description: ATPase, Na+/K+ transporting, beta 1 polypeptide [Source:HGNC Symbol;Acc:804]

Sequence

>retro_cjac_2288
ATTCTACATAATGGCTGCCTGGCTGGCCTCTTCATTAGAATCATCCAAGTGCTACTGCTCACCATCAGTGAACTGAAGCC
ACAAATCAGGACTGAGTGAACCCAGCAGGATTAACAGATTTCTCAGATCCAGAGACTGAAATTAGCTTTCATCCTAGTGA
TCCCAAGATCTATGAGGCATACGTGCTGAACATAGATAGGTTCTTGGAAAAGTACAAAGATTCAGCCCTGAAGGATGGCA
TGATTTAAGATTGTGACAGTTTGTCCAGTGTACCCAAAGAATGAGGAGACTAATCATGAATCAAGAGAGTGAAAAGTTTG
CAAATTCAAGCTTGAGTGACTGGGAAATAGCTTTGGATTAAATGATGAAACTTATGGCTACAAAGAGTGCAAACCATGCA
TTATTATACAGCTCAAATGAGTTCTAGGTTTCAAACCTAAGCCTCCCAAGAATGAGTCCTTGGAGACTTACCCAGTGATG
AAGTATGACTCATATGTCTTTCGTGTTCCGTGCACTAGCAAGCAAGATGAAGATAAGGATAAAGATGGAAATGTGGAGTA
TTTTGGAAATGACCCAGGTTTTCCTCTGCAGTGTTATTCTTACTGTGACAAACTCCTGCAGCCCAAATACCTGCAGCCCC
TGCTCTCTGTACAGTTTACCAGCCTTACCATGGACACTGAAATTCACATAGAATGTGAAGTGTGTGGTGAGAACATTGGG
TACAGTGAGAAAGATGGTTTTCAGGGATGCTTTGATATAAAAATTGAAGTTAAGAGC

Alignment

ORF - retro_cjac_2288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.68 %
• Parental protein coverage: 90.1 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VIFYGCLAGIFIGTIQVMLLTISELKP-TYQDRVAPPGLTQIPQIQKTEIAFRPNDPKSYEAYVLNIVRF
          ....GCLAG.FI..IQV.LLTISELKP.T.QD.V.P.GLT.......TEI.F.P.DPK.YEAYVLNI.RF
Retrocopy ILHNGCLAGLFIRIIQVLLLTISELKP<TNQD*VNPAGLTDFSD-PETEISFHPSDPKIYEAYVLNIDRF

Parental  LEKYKDSAQKEEMIFEDCGNV-PSEPKERGDLNHEQGERKVCRFKLEWLGNCSGLNDETYGYREGKPCII
          LEKYKDSA.K..MI..DC....P..PK.....NHE..E.KVC.FKLE.LGN..GLNDETYGY.E.KPCII
Retrocopy LEKYKDSALKDGMI*-DCDSL>PVYPKNE-ETNHESRE*KVCKFKLE*LGNSFGLNDETYGYKECKPCII

Parental  IKLNRVLGFKPKPPKNESLETYPVMKYNPYVLPVQCTGKRDEDKEKIGNVEYFGLGNYPGFPLQYYPYYG
          I.L..VLGFKPKPPKNESLETYPVMKY..YV..V.CT.K.DEDK.K.GNVEYF..GN.PGFPLQ.Y.Y..
Retrocopy IQLK*VLGFKPKPPKNESLETYPVMKYDSYVFRVPCTSKQDEDKDKDGNVEYF--GNDPGFPLQCYSYCD

Parental  KLLQPKYLQPLLAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIEVKS
          KLLQPKYLQPLL.VQFT.LTMDTEI.IEC...GENIGYSEKD.FQG.FD.KIEVKS
Retrocopy KLLQPKYLQPLLSVQFTSLTMDTEIHIECEVCGENIGYSEKDGFQGCFDIKIEVKS

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	1.66 RPM	74.99 RPM
SRP051959_heart	1.37 RPM	51.78 RPM
SRP051959_kidney	1.00 RPM	315.15 RPM
SRP051959_liver	0.71 RPM	52.20 RPM
SRP051959_lung	1.45 RPM	24.03 RPM
SRP051959_lymph_node	1.53 RPM	4.86 RPM
SRP051959_skeletal_muscle	1.75 RPM	48.74 RPM
SRP051959_spleen	1.30 RPM	13.09 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2288 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2288 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2288 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2924
Pan troglodytes	retro_ptro_1979
Gorilla gorilla	retro_ggor_2027

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001981	1 retrocopy	retro_cjac_309,
Callithrix jacchus	ENSCJAG00000010317	1 retrocopy	retro_cjac_2288 ,
Homo sapiens	ENSG00000143153	1 retrocopy	retro_hsap_2924,
Gorilla gorilla	ENSGGOG00000002499	1 retrocopy	retro_ggor_2027,
Pan troglodytes	ENSPTRG00000001653	1 retrocopy	retro_ptro_1979,
Xiphophorus maculatus	ENSXMAG00000016407	1 retrocopy	retro_xmac_22,