RetrogeneDB ID: retro_cjac_1050

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:80727952..80728451(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB11A
• Ensembl ID: ENSCJAG00000007333
• Aliases: None
• Description: RAB11A, member RAS oncogene family [Source:HGNC Symbol;Acc:9760]

Sequence

>retro_cjac_1050
TTTGCAACAAGAAACACCCAGACTGATGGGAAAACAATAAAGGCACAGATATAGGAGAGACCAGGGCAAGAATAATACCA
AGCTATAACATAAGCATATCATCGTAGAGATATAGGTGCCTTATGGTTTAAGACATTGATAAACATCTCACATATGAAAA
TATAGAGCAATTGCTGAAATGACTGAGAGATCACGCTGATAGTAACATTGTTGTAGTGTTATCATGGACAAATAAAAGTG
ATTTACATCATCTTAGGGAAGTTGAAGCAAGCGCTTTTGCAGAAAAAAAATGATTTGTCATTCAGTGAGACATCTTCTCT
AGACTCTGCAAATGTAGAATCTCCTTTTCAGGCAATTCTAACAGGATATCCCACATTGTTTCTCAGAAGCAAATGTCAGA
CAGACCCAAAACGACATGACCCCAAGCAACAATGTGGTTTCTATTCATGTTCCACCAATCACTCAAAACAAACCAGAGGT
GCAGTGCTGTCAGAACATC

Alignment

ORF - retro_cjac_1050 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.54 %
• Parental protein coverage: 64.75 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FATRSIQVDGKTIKAQIWDTAGQERYRAITSAYYRGAVGAL-LVYDIAKHLTYENVERWLKELRDHADSN
          FATR..Q.DGKTIKAQI....GQE.Y.AIT.AY.R...GAL..V.DI.KHLTYEN.E..LK.LRDHADSN
Retrocopy FATRNTQTDGKTIKAQI*ERPGQE*YQAIT*AYHRRDIGAL<MV*DIDKHLTYENIEQLLK*LRDHADSN

Parental  IVIMLVG-NKSDLRHLRAVPTDEARAFAEK-NGLSFIETSALDSTNVEAAFQTILT-EIYRIVSQKQMSD
          IV..L...NKSDL.HLR.V...EA.AFAEK.N.LSF.ETS.LDS.NVE..FQ.ILT..I..IVSQKQMSD
Retrocopy IVVVLSWTNKSDLHHLREV---EASAFAEK>NDLSFSETSSLDSANVESPFQAILT<RISHIVSQKQMSD

Parental  R-RENDMSPSNNVVPIHVPPTTENKPKVQCCQNI
          R...NDM.PSNNVV.IHVPP.T.NKP.VQCCQNI
Retrocopy R<TQNDMTPSNNVVSIHVPPITQNKPEVQCCQNI

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	78.79 RPM
SRP051959_heart	0.00 RPM	36.41 RPM
SRP051959_kidney	0.00 RPM	47.88 RPM
SRP051959_liver	0.00 RPM	37.41 RPM
SRP051959_lung	0.00 RPM	53.63 RPM
SRP051959_lymph_node	0.00 RPM	37.58 RPM
SRP051959_skeletal_muscle	0.00 RPM	31.93 RPM
SRP051959_spleen	0.00 RPM	39.56 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1050 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1050 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1050 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018959	1 retrocopy	retro_btau_1850,
Callithrix jacchus	ENSCJAG00000007333	1 retrocopy	retro_cjac_1050 ,
Callithrix jacchus	ENSCJAG00000007715	1 retrocopy	retro_cjac_1256,
Callithrix jacchus	ENSCJAG00000010778	2 retrocopies	retro_cjac_3866, retro_cjac_3917,
Echinops telfairi	ENSETEG00000004920	5 retrocopies	retro_etel_1150, retro_etel_2132, retro_etel_2214, retro_etel_694, retro_etel_837,
Homo sapiens	ENSG00000103769	1 retrocopy	retro_hsap_715,
Gorilla gorilla	ENSGGOG00000014252	2 retrocopies	retro_ggor_538, retro_ggor_605,
Myotis lucifugus	ENSMLUG00000008820	2 retrocopies	retro_mluc_1606, retro_mluc_2435,
Macaca mulatta	ENSMMUG00000008006	1 retrocopy	retro_mmul_2463,
Nomascus leucogenys	ENSNLEG00000012853	1 retrocopy	retro_nleu_467,
Petromyzon marinus	ENSPMAG00000009335	1 retrocopy	retro_pmar_25,
Pongo abelii	ENSPPYG00000006573	1 retrocopy	retro_pabe_618,
Pan troglodytes	ENSPTRG00000007188	1 retrocopy	retro_ptro_510,