RetrogeneDB ID: retro_cjac_2669

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:133213952..133214670(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCAP29
• Ensembl ID: ENSCJAG00000016329
• Aliases: None
• Description: B-cell receptor-associated protein 29 [Source:HGNC Symbol;Acc:24131]

Sequence

>retro_cjac_2669
CTCCAATGGGCGGCAGTGGCAAACTTTCTTTATGCCGAAATAGGACTCATTTTAATCTTCTGCTTACCTTTTATTCCTCC
TCAGAGATGGCAGAAGATTTTTTCACTTAATGTCTGGGGTAAAATTGCAACTTTTTGGAAAAAGCCTTTCCTTACTATTA
TCGTCCTATTGATTGTTCTATTTCTAGATGCTGTGTGAGAAGTAGGGAAATATTCCTCAGTTCATACCATTTGGAAGAGT
TCCACCAGCAGACCTGATGCATATGAACACACACAGATGAAACTTTTTAGGTCTCAAAGAAATCTTTACATTTCTGGATT
TTCTCTATTTTTTTTGGCTAGTGTTGAGATGTCTGGTTACGCTTATTACTCAACTGGCAAAAGAACTGTTAAACAAAGGT
GTACTTAAAACTCAAGCAGAAAATACTAACAAGGCTGACAAAAAATTTTTGGAAGAAAATGAAAAACTAAAACAGATTTT
GAAAAGCCATGGTAATAATGAAGAATGTGTTTGGGAAGCAGAAAATAAAAAACTAGTAGAAGACCAGGAGAAACTGAAAA
CTGAATTAAGGAAGACTTCAGATGCCCTTTCTAAGGCACAAAATGATGTGATGGCAATGAAGATGCAATCGGAGAGACTT
TCAAAAGAATATGATCAACTCCTGAAAGAACACTCTGAACTTCAGGATTGTTTAGGAAGACGCAACAAGAAAAGACTC

Alignment

ORF - retro_cjac_2669 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.5 %
• Parental protein coverage: 99.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQWAAVATFLYAEIGLILIFCLPFIPPQRWQKIFSFNVWGKIATLWNKAFLTIIILLIVLFLDAVREVRK
          LQWAAVA.FLYAEIGLILIFCLPFIPPQRWQKIFS.NVWGKIAT.W.K.FLTII.LLIVLFLDAV.EV.K
Retrocopy LQWAAVANFLYAEIGLILIFCLPFIPPQRWQKIFSLNVWGKIATFWKKPFLTIIVLLIVLFLDAV*EVGK

Parental  YSSVHTIEKSSTSRPDAYEHTQMKLFRSQRNLYISGFSLFF-WLVLRRLVTLITQLAKELSNKGVLKTQA
          YSSVHTI.KSSTSRPDAYEHTQMKLFRSQRNLYISGFSLFF.WLVLR.LVTLITQLAKEL.NKGVLKTQA
Retrocopy YSSVHTIWKSSTSRPDAYEHTQMKLFRSQRNLYISGFSLFF>WLVLRCLVTLITQLAKELLNKGVLKTQA

Parental  ENTSKAAKKFLEENEKLKRILKSRGNNEECVLEAENKKLVEDQEKLKTELRKTSDALSKAQNDVMAMKMQ
          ENT.KA.KKFLEENEKLK.ILKS.GNNEECV.EAENKKLVEDQEKLKTELRKTSDALSKAQNDVMAMKMQ
Retrocopy ENTNKADKKFLEENEKLKQILKSHGNNEECVWEAENKKLVEDQEKLKTELRKTSDALSKAQNDVMAMKMQ

Parental  SERLSKEYDQLLKEHSELQDCLGRGNKKRL
          SERLSKEYDQLLKEHSELQDCLGR.NKKRL
Retrocopy SERLSKEYDQLLKEHSELQDCLGRRNKKRL

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	0.02 RPM	19.77 RPM
SRP051959_heart	0.00 RPM	24.38 RPM
SRP051959_kidney	0.02 RPM	10.01 RPM
SRP051959_liver	0.00 RPM	6.37 RPM
SRP051959_lung	0.03 RPM	7.97 RPM
SRP051959_lymph_node	0.07 RPM	5.39 RPM
SRP051959_skeletal_muscle	0.00 RPM	15.18 RPM
SRP051959_spleen	0.00 RPM	7.69 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2669 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2669 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2669 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011348	1 retrocopy	retro_cjac_2552,
Callithrix jacchus	ENSCJAG00000016329	1 retrocopy	retro_cjac_2669 ,
Echinops telfairi	ENSETEG00000008025	1 retrocopy	retro_etel_194,
Oryctolagus cuniculus	ENSOCUG00000027511	1 retrocopy	retro_ocun_235,
Otolemur garnettii	ENSOGAG00000013116	1 retrocopy	retro_ogar_2169,