RetrogeneDB ID: retro_cjac_3104

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:127378331..127379062(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3I
• Ensembl ID: ENSCJAG00000006810
• Aliases: None
• Description: None

Sequence

>retro_cjac_3104
ACAGGCAAGTAGTTGGCCCTACTCAAAACTGATTGAGCTGTTCAGACCTCTGGCAAGGACTTTGGGGGCAATATCACCAT
GTCCTCCACAGACAAGCAGATGGGCTACCAGTGCTTTGTGAGCTTCCTTAATCTGCAGGATTTAAGCCAGACTGACAACA
ATGAGACCTACATGAAAATCGATTACAATGACTATAATATCACTAGTGCTTTTGAGGACCCCTCCACCCAGGGGAGTGTA
TCATCACAGGCCATAAGAGTGGAGTGTCTAGTCAGTATAGTGCCAAGCCTGTAGTGATATTGGTGAATGTTAAACAGCAC
TCCCAGAAGATCAGTGACATCCAGTTATCCAGAGACACGACCATGTTTGTCACTGCATCCAAGGACAACACAGCCAAGTT
CTTCGATTCTACAACTCTTGAATATCAGGAGACTCTGGACAGAACATCCCATCAACTCAGCTGCCCTTTCCCCAACTATA
ATGACCATGTGATACTGGGTAACAGAGAGAAAGTCATGGATGTAACCACAACTTCCAACAGGACTGGCAGGTTTGAGGCT
AGGTTCTTTCATTTGGCCTTCGAAAAAAAGTTTGGATGAGTCAGAGATTACTTCATAATTGTAAACAGGGTTGCCCTCCA
ATCTAATGGCAAGAGTTACGGCAGCAGCAGTAAAGATGGTTATCTCCATATTTACTATTTAGGCCCACAGTCCTCTAAAT
TTGAGCTTGAG

Alignment

ORF - retro_cjac_3104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.86 %
• Parental protein coverage: 74.46 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TGKQLALLKTNSAVRTCGFDFGGNIIMFSTDKQMGYQCFVSFFDLRDPSQIDNNEPYMKIPCNDSKITSA
          TGK.LALLKT..AV.T.G.DFGGNI.M.STDKQMGYQCFVSF..L.D.SQ.DNNE.YMKI..ND..ITSA
Retrocopy TGK*LALLKTD*AVQTSGKDFGGNITMSSTDKQMGYQCFVSFLNLQDLSQTDNNETYMKIDYNDYNITSA

Parental  VW-GPL--GECIIAGHESGELNQYSAKSGEVLVNVKEHSRQINDIQLSRDMTMFVTASKDNTAKLFDSTT
          ...GPL..GECII.GH.SG...QYSAK....LVNVK.HS..I.DIQLSRD.TMFVTASKDNTAK.FDSTT
Retrocopy FE<GPLHPGECIITGHKSGVSSQYSAKPVVILVNVKQHSQKISDIQLSRDTTMFVTASKDNTAKFFDSTT

Parental  LEHQKTFRTERPVNSAALSPNYDHVVLGGGQEAMDVTTTSTRIGKFEARFFHLAFEEEFGRVKGHFGPIN
          LE.Q.T........S.......DHV.LG.....MDVTTTS.R.G.FEARFFHLAFE..FG.V...F...N
Retrocopy LEYQETLDRTSHQLSCPFPNYNDHVILGNREKVMDVTTTSNRTGRFEARFFHLAFEKKFG*VRDYFIIVN

Parental  SVAFHPDGKSYSSGGEDGYVRIHYFDPQYFEFEFE
          .VA....GKSY.S...DGY..I.Y..PQ...FE.E
Retrocopy RVALQSNGKSYGSSSKDGYLHIYYLGPQSSKFELE

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	24.30 RPM
SRP051959_heart	0.00 RPM	29.17 RPM
SRP051959_kidney	0.00 RPM	33.10 RPM
SRP051959_liver	0.00 RPM	34.22 RPM
SRP051959_lung	0.00 RPM	23.28 RPM
SRP051959_lymph_node	0.00 RPM	26.46 RPM
SRP051959_skeletal_muscle	0.00 RPM	54.14 RPM
SRP051959_spleen	0.00 RPM	30.36 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3104 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3104 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010674	1 retrocopy	retro_cfam_321,
Callithrix jacchus	ENSCJAG00000006810	1 retrocopy	retro_cjac_3104 ,
Callithrix jacchus	ENSCJAG00000021593	1 retrocopy	retro_cjac_2503,
Echinops telfairi	ENSETEG00000008047	1 retrocopy	retro_etel_1497,
Homo sapiens	ENSG00000084623	2 retrocopies	retro_hsap_3888, retro_hsap_3894,
Gorilla gorilla	ENSGGOG00000001579	3 retrocopies	retro_ggor_2540, retro_ggor_2615, retro_ggor_2623,
Loxodonta africana	ENSLAFG00000017026	1 retrocopy	retro_lafr_1073,
Macaca mulatta	ENSMMUG00000006119	2 retrocopies	retro_mmul_1730, retro_mmul_1733,
Monodelphis domestica	ENSMODG00000017481	2 retrocopies	retro_mdom_1054, retro_mdom_822,
Mus musculus	ENSMUSG00000028798	2 retrocopies	retro_mmus_1375, retro_mmus_607,
Nomascus leucogenys	ENSNLEG00000002426	2 retrocopies	retro_nleu_1129, retro_nleu_1135,
Pongo abelii	ENSPPYG00000001598	2 retrocopies	retro_pabe_3169, retro_pabe_3175,
Rattus norvegicus	ENSRNOG00000047185	1 retrocopy	retro_rnor_1548,