RetrogeneDB ID: retro_cjac_1715

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:46438232..46438752(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB22A
• Ensembl ID: ENSCJAG00000019039
• Aliases: None
• Description: None

Sequence

>retro_cjac_1715
GTGTGGTGGTTTGTGGAAGACCGTTTTGATCCAAACATCAACCCAACAATGGGGGCATCTTTTATGACCAAGACTGTCCA
GTACCAACATGAGCTGCCGTAAATTTCTAATCTGGGGTACAGCTGGACAAGAACGATTTCGTGCCTTAGCACCAATGTCC
TGTCGAGGGTCGGCCGCAGCTATAATCGTTTATGATATCACAAAAGAAGAGACATTTTCAACATGAAAGAATTGGGTGAA
AGAGCTTGGACAGCATGGCCCACATAATATTGCAGTTGCCATTGCAGGAAGTAAGTGTGATCATATTGATGTAAGAGAAT
TCATGGAGAGAGATGCAAAGGACTATGCCGACCTTATTCATGCAATTTTTGCAGAGACCAGCGCAAAAAACGTGATAAAC
ATAAGTGAACTCTTTACAGAAATTAGTCAAAGAATTCCATCCACCGACGCCAACCCGCCTTCTGGTGGCAAGGGTTTCAA
ACTCCGAAGGCAGCCTTCAGAGCCAAAGCGGAGCTGCTGC

Alignment

ORF - retro_cjac_1715 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.36 %
• Parental protein coverage: 92.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VWRFVEDSFDPNINPTIGASFMTKTVQYQNEL-HKFLIWDTAGQERFRALAPMYYRGSAAAIIVYDITKE
          VW.FVED.FDPNINPT.GASFMTKTVQYQ.EL..KFLIW.TAGQERFRALAPM..RGSAAAIIVYDITKE
Retrocopy VWWFVEDRFDPNINPTMGASFMTKTVQYQHEL>RKFLIWGTAGQERFRALAPMSCRGSAAAIIVYDITKE

Parental  ETFSTLKNWVKELRQHGPPNIVVAIAGNKCDLIDVREVMERDAKDYADSIHAIFVETSAKNAININELFI
          ETFST.KNWVKEL.QHGP.NI.VAIAG.KCD.IDVRE.MERDAKDYAD.IHAIF.ETSAKN.INI.ELF.
Retrocopy ETFST*KNWVKELGQHGPHNIAVAIAGSKCDHIDVREFMERDAKDYADLIHAIFAETSAKNVINISELFT

Parental  EISRRIPSTDANPPSGGKGFKLRRQPSEPKRSCC
          EIS.RIPSTDANPPSGGKGFKLRRQPSEPKRSCC
Retrocopy EISQRIPSTDANPPSGGKGFKLRRQPSEPKRSCC

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	11.56 RPM
SRP051959_heart	0.00 RPM	11.54 RPM
SRP051959_kidney	0.00 RPM	11.87 RPM
SRP051959_liver	0.02 RPM	8.38 RPM
SRP051959_lung	0.03 RPM	13.57 RPM
SRP051959_lymph_node	0.00 RPM	13.84 RPM
SRP051959_skeletal_muscle	0.00 RPM	10.83 RPM
SRP051959_spleen	0.00 RPM	13.49 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1715 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1715 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1715 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012646	1 retrocopy	retro_amel_617,
Canis familiaris	ENSCAFG00000012101	1 retrocopy	retro_cfam_501,
Callithrix jacchus	ENSCJAG00000000472	2 retrocopies	retro_cjac_189, retro_cjac_1948,
Callithrix jacchus	ENSCJAG00000003731	1 retrocopy	retro_cjac_3268,
Callithrix jacchus	ENSCJAG00000004529	2 retrocopies	retro_cjac_1178, retro_cjac_1179,
Callithrix jacchus	ENSCJAG00000007527	2 retrocopies	retro_cjac_1215, retro_cjac_1879,
Callithrix jacchus	ENSCJAG00000019039	2 retrocopies	retro_cjac_1715 , retro_cjac_842,
Microcebus murinus	ENSMICG00000008382	1 retrocopy	retro_mmur_1546,
Oryctolagus cuniculus	ENSOCUG00000004414	1 retrocopy	retro_ocun_554,
Otolemur garnettii	ENSOGAG00000015779	1 retrocopy	retro_ogar_2851,