RetrogeneDB ID: retro_cjac_2940

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:125450546..125451175(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPNS1
• Ensembl ID: ENSCJAG00000009594
• Aliases: None
• Description: calpain, small subunit 1 [Source:HGNC Symbol;Acc:1481]

Sequence

>retro_cjac_2940
GCCATGTTCTTCCTAGGTGGAGTCATTAGCTCCATCAGGGAGGTGGCTACACAGCACAACCCAGAACCCCTGCCTCCACA
CACACATTGCTCCAACACTGAGGCCAACAAGAGTGAGGAGGTCCATCATTCCAGAGACTCTTTACCCAGTTGGCTGGGGA
TGAAATTGAGGTCAGGTTTGCAGAACTCATGAATGTTCTCAATAAGACTGTGATCAGTATGACTGAATGGAAGACTCATG
GCTTTAGCATTGATACATGGCACAGCATGGTGGCTACAATGGATAGTGACACCACAGGCAAGTTGGGCTTTGAGGAATTA
GGTTAGCTGTGGAACAACATCAAAAGGTGACAGGCAATATACAAGCAGTTGGATGTTGACTGATTGGGAACCATTTCCAG
CAGTGAACTCACAGGGCCTTTGAGGCAGCAGGGTTTCACCTGAATGAGCAACTCTGCAACACAATCATCTGACACTACTT
AGATGAAGGAGGGAACATGGATTTCAACAACTTTATCAGCTGCTTAGTCAGGCTGGATGCTTTTGTTTCATGGCTTGAAA
TTTCTTGACAAAGATGACACTAGATCAATCCAAGTGAATATCCAAGAACGACTGCAGCTGACAATGTAT

Alignment

ORF - retro_cjac_2940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.48 %
• Parental protein coverage: 88.98 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AMRILGGVISAISEAAAQYNPEPPPPRTHYSNIEANESEEVRQ-FRRLFAQLAGDDMEVSATELMNILNK
          AM..LGGVIS.I.E.A.Q.NPEP.PP.TH.SN.EAN.SEEV...F.RLF.QLAGD..EV...ELMN.LNK
Retrocopy AMFFLGGVISSIREVATQHNPEPLPPHTHCSNTEANKSEEVHH<FQRLFTQLAGDEIEVRFAELMNVLNK

Parental  VVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKRWQGIYKQFDTDRSGTICSSELPG
          .V......KT.GF.IDT..SMVA.MDSDTTGKLGFEE...LWNNIKR.Q.IYKQ.D.D..GTI.SSEL.G
Retrocopy TVISMTEWKTHGFSIDTWHSMVATMDSDTTGKLGFEELG*LWNNIKR*QAIYKQLDVD*LGTISSSELTG

Parental  -AFEAAGFHLNEHLYNMIIRRYSDESGNMDFDNFISCLVRLDA-MFRAFKSLDKDGTGQIQVNIQEWLQL
          .AFEAAGFHLNE.L.N.II..Y.DE.GNMDF.NFISCLVRLDA..F...K.LDKD.T..IQVNIQE.LQL
Retrocopy <AFEAAGFHLNEQLCNTII*HYLDEGGNMDFNNFISCLVRLDA>LFHGLKFLDKDDTRSIQVNIQERLQL

Parental  TMY
          TMY
Retrocopy TMY

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	59.82 RPM
SRP051959_heart	0.00 RPM	60.83 RPM
SRP051959_kidney	0.00 RPM	61.10 RPM
SRP051959_liver	0.00 RPM	27.53 RPM
SRP051959_lung	0.00 RPM	61.28 RPM
SRP051959_lymph_node	0.02 RPM	32.78 RPM
SRP051959_skeletal_muscle	0.00 RPM	33.43 RPM
SRP051959_spleen	0.02 RPM	31.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2940 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2940 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2940 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 26 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000000511	1 retrocopy	retro_acar_205,
Ailuropoda melanoleuca	ENSAMEG00000001024	1 retrocopy	retro_amel_136,
Bos taurus	ENSBTAG00000014872	2 retrocopies	retro_btau_1126, retro_btau_692,
Canis familiaris	ENSCAFG00000031314	1 retrocopy	retro_cfam_942,
Callithrix jacchus	ENSCJAG00000009594	1 retrocopy	retro_cjac_2940 ,
Cavia porcellus	ENSCPOG00000000115	1 retrocopy	retro_cpor_1131,
Equus caballus	ENSECAG00000012210	1 retrocopy	retro_ecab_707,
Felis catus	ENSFCAG00000014149	1 retrocopy	retro_fcat_1691,
Homo sapiens	ENSG00000126247	1 retrocopy	retro_hsap_98,
Gorilla gorilla	ENSGGOG00000003699	2 retrocopies	retro_ggor_1241, retro_ggor_263,
Myotis lucifugus	ENSMLUG00000024944	1 retrocopy	retro_mluc_2336,
Macaca mulatta	ENSMMUG00000000249	2 retrocopies	retro_mmul_1334, retro_mmul_1567,
Monodelphis domestica	ENSMODG00000014179	1 retrocopy	retro_mdom_410,
Mustela putorius furo	ENSMPUG00000005617	1 retrocopy	retro_mputfur_444,
Mus musculus	ENSMUSG00000001794	1 retrocopy	retro_mmus_80,
Nomascus leucogenys	ENSNLEG00000011712	2 retrocopies	retro_nleu_1328, retro_nleu_992,
Ornithorhynchus anatinus	ENSOANG00000002736	1 retrocopy	retro_oana_113,
Pongo abelii	ENSPPYG00000009898	2 retrocopies	retro_pabe_1359, retro_pabe_448,
Pelodiscus sinensis	ENSPSIG00000012793	1 retrocopy	retro_psin_45,
Pan troglodytes	ENSPTRG00000010887	2 retrocopies	retro_ptro_1112, retro_ptro_168,
Pteropus vampyrus	ENSPVAG00000012885	3 retrocopies	retro_pvam_1375, retro_pvam_639, retro_pvam_737,
Rattus norvegicus	ENSRNOG00000045747	2 retrocopies	retro_rnor_1447, retro_rnor_2145,
Sorex araneus	ENSSARG00000004266	1 retrocopy	retro_sara_215,
Sus scrofa	ENSSSCG00000030149	2 retrocopies	retro_sscr_495, retro_sscr_73,
Ictidomys tridecemlineatus	ENSSTOG00000026235	1 retrocopy	retro_itri_342,
Vicugna pacos	ENSVPAG00000008074	1 retrocopy	retro_vpac_64,