RetrogeneDB ID: retro_cjac_2316

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:30336578..30337277(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ETF1
• Ensembl ID: ENSCJAG00000006776
• Aliases: None
• Description: None

Sequence

>retro_cjac_2316
CGGAAAGTAGAAGAGACTGCTGTGCAGCTGTTTATTTCTGGGGACAAAGTGAATGTGGCTGGTCTAGTTTTAGCTGGATC
CACTGACTTTAAAACTGAACTAAGTCAATCTGATATGTTTGATCAGAGGTTACAATGGAAAGTTTTAAAAATAGTTGATA
TATCATTTGGTGGTGAAAATTGATTCAACCAAGCTATGGAGTTATCAACTGAAGTCCTCTCCAACATGAAATTCATTCAA
GAGAAGAAATTAATAGGACTATACTTTGATGAAATCAGCCAGGACACAGGCAAGTACTGTTTGGGTGCTGAAAATACACT
AAAGGCTTTGGAATGGGAGCTGTAGAAATTCTAATAGTATATGAAAATCTGGATATAATGAGATATGTTCTTCATTGCAA
GGCACAGAAGAGAAGAAAATTCTCTAAGTCCAGAGCAAGAAAAGGATAAATGTCATTTTGCAGACAAAGAGACCAGACAG
GAACATGAGCTTATCAAGAGCATGCCCCTGTTGGAATGGTTTCCTAACAACTATAAAAAATTTGGAGCTAGGTTGGAAAT
TGTCACAGATAAATCACAAGAAGGGTCTCAGTTTGTAAAAGGATTTGGTGGAATTGGAGGTATCTTGTGGTATTGGGTAG
ATTTCCAGGGAATGGAATACCAAGGAAGAGATCATGAATTTTTTGACCTTGATGACTAC

Alignment

ORF - retro_cjac_2316 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.39 %
• Parental protein coverage: 58.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RKVAETAVQLFISGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLVDISYGGENGFNQAIELST
          RKV.ETAVQLFISGDKVNVAGLVLAGS.DFKTELSQSDMFDQRLQ.KVLK.VDIS.GGEN.FNQA.ELST
Retrocopy RKVEETAVQLFISGDKVNVAGLVLAGSTDFKTELSQSDMFDQRLQWKVLKIVDISFGGEN*FNQAMELST

Parental  EVLSNVKFIQEKKLIGRYFDEISQDTGKYCFGVEDTLKALE-MGAVEILIVYENLDIMRYVLHC-QGTEE
          EVLSN.KFIQEKKLIG.YFDEISQDTGKYC.G.E.TLKALE.MGAVEILIVYENLDIMRYVLHC.QGTE.
Retrocopy EVLSNMKFIQEKKLIGLYFDEISQDTGKYCLGAENTLKALE<MGAVEILIVYENLDIMRYVLHC<QGTE-

Parental  EKILY-LTPEQEKDKSHFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGI
          EK....L.PEQEKDK.HF.DKET.QEHELI.SMPLLEWF.NNYKKFGA.LEIVTDKSQEGSQFVKGFGGI
Retrocopy EKKIL<LSPEQEKDKCHFADKETRQEHELIKSMPLLEWFPNNYKKFGARLEIVTDKSQEGSQFVKGFGGI

Parental  GGILRYRVDFQGMEYQGGDDEFFDLDDY
          GGIL.Y.VDFQGMEYQG.D.EFFDLDDY
Retrocopy GGILWYWVDFQGMEYQGRDHEFFDLDDY

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	0.13 RPM	60.99 RPM
SRP051959_heart	0.23 RPM	47.31 RPM
SRP051959_kidney	0.18 RPM	74.10 RPM
SRP051959_liver	0.04 RPM	66.71 RPM
SRP051959_lung	0.26 RPM	58.03 RPM
SRP051959_lymph_node	0.27 RPM	42.42 RPM
SRP051959_skeletal_muscle	0.04 RPM	92.35 RPM
SRP051959_spleen	0.13 RPM	64.08 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2316 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2316 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2316 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001282	1 retrocopy	retro_cfam_99,
Callithrix jacchus	ENSCJAG00000006776	2 retrocopies	retro_cjac_2316 , retro_cjac_4133,
Dasypus novemcinctus	ENSDNOG00000010830	3 retrocopies	retro_dnov_1925, retro_dnov_2504, retro_dnov_610,
Equus caballus	ENSECAG00000013041	1 retrocopy	retro_ecab_740,
Echinops telfairi	ENSETEG00000007362	2 retrocopies	retro_etel_1237, retro_etel_1400,
Gorilla gorilla	ENSGGOG00000000657	4 retrocopies	retro_ggor_2326, retro_ggor_2561, retro_ggor_2562, retro_ggor_2919,
Macaca mulatta	ENSMMUG00000005871	2 retrocopies	retro_mmul_1658, retro_mmul_718,
Mustela putorius furo	ENSMPUG00000009338	1 retrocopy	retro_mputfur_1448,
Oryctolagus cuniculus	ENSOCUG00000006650	3 retrocopies	retro_ocun_1188, retro_ocun_1614, retro_ocun_462,
Rattus norvegicus	ENSRNOG00000019450	1 retrocopy	retro_rnor_2935,