RetrogeneDB ID: retro_cjac_2514

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:43718821..43720462(+)
• Located in intron of: ENSCJAG00000000466

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLYR1
• Ensembl ID: ENSCJAG00000019912
• Aliases: None
• Description: None

Sequence

>retro_cjac_2514
ATGGCAGCTGTGAATCCGCTGTTTATCGACTTGGTGTGGGGGAAACTCAGCCAGTATCCTCCTTGGCCAGGAAAGATTGT
TAACCCATCAAAGGACTTGAAGAAACCTCGTGGAAAGAAATGCTTCTTTGTGGAACTTTTTGGAACAGAAGATCATGCCT
GGATCAGAATGAAACAACTGAAGCCATGTCATGCTCATAAAGAGGAAATGATAAAGATTAGCAAGGGTAGACTATTCCAG
CAAGTGGTGGATGCTATCAGAGAGTTTCTCAGGAGAGCCCAAAGGGAAAGACCAGACATCATCCTACAATTCTGCTAATG
ACAAGAATCGGCATAATTCCAGTGAGGAGAGAAGTAGGCCAAACTCAGGAGACGAGAGCGAAAACTTAGCCTGTCTGAAG
GGAAAGTGAGGAAGAAAATGGGAGAAGGAAAGAAGAGGATGTCTTCAGCCTCTTCAGAGAGAGGCACCAAATCCCCTCTG
AAAAGAGCCCCAAGAGCAAAGTCCCTGGATGTGGGGTCAGCTCCCAAAGGATGAGAAGACTCTTAACATCCCTGAGTCTA
GTACTGTGAAGTGGATAATGGCTGGACCGATGGCCACGTTTAAATGGCAGCCAACCACAGATGAGTCTGTTAAAGATGCA
GATCCTCATTTGCATCACTTCCTACTAAGCCAAACAGAGAAGCCAGCTGTCTGTTACTAGGAAATCGCAGAGAAGTTTAA
AATGTGTGAAGAGGAAGCTGGTTCCACCTCCATCCGGGCAGCCGACAGCACGGCTATGAATGGCAGCATCACAAACAAAA
AGATAGGATTTGGAGGCTTTGGTCTCATGGGAAGTGGAATCGTCTCCAACTTGCTAAAAATTGGTCACATAGTGACTATT
TGGAACTGCACTGCAAAGAAATGTGATTTGTTCATCTAGGAGGGGCCTGCCTGGGAAGAACGCCCGCAGAAGCCTTCTCA
ACCTGTGATATCTCTTTCACCTGCATGTCGGATCCCGAGGCAGCCAAGGACCTGGTGCTGGGCCCCAGTGGTGTGCAGCA
AGGAATCCATTCTGGGAAGTGCTATGTGGACATGTCAACAGTGGACACTGACATAGTCACTGAGCTGGCCCAGGTGAAGT
GTCCAGTTTAGGGGGGCGCTTTCCAGAAGCTGCCATCTCAGGGAATCAGCAGCTGTCTAATCACGGGATGTTAGTGATCT
TAGCAGCTGGAGACGGGCTAATATGAGGACTGTGGCATCTGCTTCCAGGCAATGGAGAAGACCTCCTTCCTAGGTGAAAT
TGGCAACACAGCCAAGATGGTGCTGATCATGAACATGGTCCAAGGGAGCTTCATGGTCACCGTCGCTGAGGAGCTGACTC
TGGCCCAGATAACAGGCCAGTCCCAGCAGACACTCTTGGACATCCTCAATCAGGGACAATTGACCAGCATCTTCCTAGAC
CAGAAGTGCCAAAATATCCTGCAAGGAAACTTTAAGCCTGATTTCTTCCTGAAATACATTCAGAAGGATCTCCGCTTAGC
CATTGCGCTGGGCAATGTGGTCAACCATCTGACTTCCATGGCAGCTGCAGCCAATGAGGTGTACAGAAGAGCGAAGGCAC
TGGACCAGTCGACAATGTCCACCGTGTACTGAGCCTACATA

Alignment

ORF - retro_cjac_2514 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.71 %
• Parental protein coverage: 99.82 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MAAVSLRLGDLVWGKLGRYPPWPGKIVNPPKDLKKPRGKKCFFVKFFGTEDHAWIKVEQLKPYHAHKEEM
          MAAV.....DLVWGKL..YPPWPGKIVNP.KDLKKPRGKKCFFV..FGTEDHAWI...QLKP.HAHKEEM
Retrocopy MAAVNPLFIDLVWGKLSQYPPWPGKIVNPSKDLKKPRGKKCFFVELFGTEDHAWIRMKQLKPCHAHKEEM

Parental  IKINKGKRFQQAVDAVEEFLRRA-KGKDQTSSHNSADDKNRRNSSEERSRPNSGDE-KRKLSLSEGKVKK
          IKI.KG..FQQ.VDA..EFLRRA.KGKDQTSS.NSA.DKNR.NSSEERSRPNSGDE..RKLSLSEGKV.K
Retrocopy IKISKGRLFQQVVDAIREFLRRA>KGKDQTSSYNSANDKNRHNSSEERSRPNSGDE<ERKLSLSEGKVRK

Parental  NVGEGKKRVSSGSSERGSKSPLKRA-QEQSPRKRGRPPKDEKDLTIPESSTVKGMMAGPMATFKWQPTAS
          ..GEGKKR.SS.SSERG.KSPLKRA.QEQSP...G..PKDEK.L.IPESSTVK..MAGPMATFKWQPT..
Retrocopy KMGEGKKRMSSASSERGTKSPLKRA>QEQSPWMWGQLPKDEKTLNIPESSTVKWIMAGPMATFKWQPTTD

Parental  EPVKDADPHFHHFLLSQTEKPAVCYQAITKKLKICEEETGSTSIQAADSTAVNGSITPTDKKIGFLGLGL
          E.VKDADPH.HHFLLSQTEKPAVCY..I..K.K.CEEE.GSTSI.AADSTA.NGSI..T.KKIGF.G.GL
Retrocopy ESVKDADPHLHHFLLSQTEKPAVCY*EIAEKFKMCEEEAGSTSIRAADSTAMNGSI--TNKKIGFGGFGL

Parental  MGSGIVSNLLKMGHTVTVWNRTAEKCDLFIQE-GARLGRTPAEVVSTCDITFACVSDPKAAKDLVLGPSG
          MGSGIVSNLLK.GH.VT.WN.TA.KCDLFI.E.GA.LGRTPAE..STCDI.F.C.SDP.AAKDLVLGPSG
Retrocopy MGSGIVSNLLKIGHIVTIWNCTAKKCDLFI*E<GACLGRTPAEAFSTCDISFTCMSDPEAAKDLVLGPSG

Parental  VLQGIRPGKCYVDMSTVDADTVTELAQVIVSRGG-RFLEAPVSG-NQQLSNDGMLVILAAGDRGL-YEDC
          V.QGI..GKCYVDMSTVD.D.VTELAQV.....G..F...P..G.NQQLSN.GMLVILAAGD.GL.YEDC
Retrocopy VQQGIHSGKCYVDMSTVDTDIVTELAQVKCPV*GGAFQKLPSQG<NQQLSNHGMLVILAAGD-GL>YEDC

Parental  SSCFQAMGKTSFFLGEVGNAAKMMLIVNMVQGSFMATIAEGLTLAQVTGQSQQTLLDILNQGQLASIFLD
          ..CFQAM.KTS.FLGE.GN.AKM.LI.NMVQGSFM.T.AE.LTLAQ.TGQSQQTLLDILNQGQL.SIFLD
Retrocopy GICFQAMEKTS-FLGEIGNTAKMVLIMNMVQGSFMVTVAEELTLAQITGQSQQTLLDILNQGQLTSIFLD

Parental  QKCQNILQGNFKPDFYLKYIQKDLRLAIALGDAVNHPTPMAAAANEVYKRAKALDQSDNDMSAVYRAYI
          QKCQNILQGNFKPDF.LKYIQKDLRLAIALG..VNH.T.MAAAANEVY.RAKALDQS...MS.VY.AYI
Retrocopy QKCQNILQGNFKPDFFLKYIQKDLRLAIALGNVVNHLTSMAAAANEVYRRAKALDQS--TMSTVY*AYI

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	2.40 RPM	27.49 RPM
SRP051959_heart	0.65 RPM	23.42 RPM
SRP051959_kidney	1.13 RPM	41.55 RPM
SRP051959_liver	1.02 RPM	24.30 RPM
SRP051959_lung	2.33 RPM	33.25 RPM
SRP051959_lymph_node	2.83 RPM	34.38 RPM
SRP051959_skeletal_muscle	0.59 RPM	22.73 RPM
SRP051959_spleen	1.70 RPM	32.84 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2514 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2514 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2514 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1512

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019912	1 retrocopy	retro_cjac_2514 ,
Erinaceus europaeus	ENSEEUG00000011783	1 retrocopy	retro_eeur_477,
Homo sapiens	ENSG00000140632	1 retrocopy	retro_hsap_2432,
Gorilla gorilla	ENSGGOG00000016258	1 retrocopy	retro_ggor_1512,
Macaca mulatta	ENSMMUG00000009567	1 retrocopy	retro_mmul_621,
Nomascus leucogenys	ENSNLEG00000009950	1 retrocopy	retro_nleu_240,
Oryctolagus cuniculus	ENSOCUG00000010486	1 retrocopy	retro_ocun_680,
Pongo abelii	ENSPPYG00000007072	1 retrocopy	retro_pabe_1791,
Pan troglodytes	ENSPTRG00000007730	1 retrocopy	retro_ptro_1404,