RetrogeneDB ID: retro_cjac_1745

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:26430860..26431331(-)
• Located in intron of: ENSCJAG00000016986

Retrocopy information

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

Parental gene information

• Parental gene symbol: PEF1
• Ensembl ID: ENSCJAG00000006355
• Aliases: PEF1, peflin
• Description: None

Sequence

>retro_cjac_1745
CAGTCAGTGGAGTCCAATCACAGTGGCTCTCTCCATAAAGAGGTGAAGCAGGCCCTGGTCAACTTCAATTGATCCTCGTT
TAATGATGAGACCTGCCTTATGATGATAAACATTTTTGACGAGACCAAGTCTGGCTGCATCAATGTCTATGGCTTCTCAA
CCCTGTGGAAATTCATCCAGCAGTGGAAGACACTCTTCCAGCAGTATAACAGGGACCACTCAGGCTCCATTAGCTACAGA
GCTGCAGCAAGCTCTGTCCCAAATGGACTACAACCCCAGTTTACCCAGCTTCTGGTCTCCTGCTACTGCTCACACTCTGC
CAATCCTCCCATGCAGCTTGACTGCTTTATCCAGGTGTGCACTCAGCTCCAGGTGCTGATGAAGGCCTTTCGGTAGAAGG
ACACAGCTACACAAGGCAACACCCAGCTCAGCTTCCAGAACTTTGTCACCATAACAGCTTCTTGGATGCTA

Alignment

ORF - retro_cjac_1745 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.67 %
• Parental protein coverage: 56.69 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QSVDSDHSGYISMKELKQALVNCNWSSFNDETCLMMINMFDKTKSGRIDVYGFSALWKFIQQWKNLFQQY
          QSV.S.HSG....KE.KQALVN.N.SSFNDETCLMMIN.FD.TKSG.I.VYGFS.LWKFIQQWK.LFQQY
Retrocopy QSVESNHSGSLH-KEVKQALVNFN*SSFNDETCLMMINIFDETKSGCINVYGFSTLWKFIQQWKTLFQQY

Parental  DRDRSGSISYTELQQALSQMGYNLSPQFTQLLVSRYCPRSANPAMQLDRFIQVCTQLQVLTEAFREKDTA
          .RD.SGSISY.....A.S.....L.PQFTQLLVS.YC..SANP.MQLD.FIQVCTQLQVL..AFR.KDTA
Retrocopy NRDHSGSISY---RAAASSVPNGLQPQFTQLLVSCYCSHSANPPMQLDCFIQVCTQLQVLMKAFR*KDTA

Parental  VQGNIRLSFEDFVTMTASRML
          .QGN..LSF..FVT.TAS.ML
Retrocopy TQGNTQLSFQNFVTITASWML

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	0.95 RPM	12.07 RPM
SRP051959_heart	0.81 RPM	10.70 RPM
SRP051959_kidney	1.09 RPM	18.55 RPM
SRP051959_liver	0.80 RPM	11.74 RPM
SRP051959_lung	1.63 RPM	13.65 RPM
SRP051959_lymph_node	2.08 RPM	9.43 RPM
SRP051959_skeletal_muscle	0.74 RPM	9.87 RPM
SRP051959_spleen	1.07 RPM	10.23 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1745 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1745 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1745 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006355	1 retrocopy	retro_cjac_1745 ,
Homo sapiens	ENSG00000162517	1 retrocopy	retro_hsap_497,
Gorilla gorilla	ENSGGOG00000015897	1 retrocopy	retro_ggor_464,
Macropus eugenii	ENSMEUG00000014458	1 retrocopy	retro_meug_375,
Microcebus murinus	ENSMICG00000001374	1 retrocopy	retro_mmur_937,
Macaca mulatta	ENSMMUG00000023397	1 retrocopy	retro_mmul_146,
Monodelphis domestica	ENSMODG00000017573	1 retrocopy	retro_mdom_1930,
Nomascus leucogenys	ENSNLEG00000001979	1 retrocopy	retro_nleu_2422,
Oryctolagus cuniculus	ENSOCUG00000005744	1 retrocopy	retro_ocun_461,
Pongo abelii	ENSPPYG00000001611	1 retrocopy	retro_pabe_238,
Pan troglodytes	ENSPTRG00000000463	1 retrocopy	retro_ptro_375,
Rattus norvegicus	ENSRNOG00000013972	2 retrocopies	retro_rnor_1563, retro_rnor_2505,