RetrogeneDB ID: retro_cjac_2965

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:18073624..18073995(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000013336
• Aliases: None
• Description: None

Sequence

>retro_cjac_2965
ATGACAGTGGCTGCATTTGGAGCACTGAACGGTCTTCGGCTAGATTGAAGGAAACTCAGAACATGGTCTGGTCCAAATCA
AGAAATGTACAGATTTTGAATATGGTGACTAGGCAAGGGGCACTTTGGACTAATACTCTAGGTTCTCTGGCTTTTCTCTG
TAGTGCATTTGGTGTCATTATTGAGAAAACATGAGGTGCAGAAGATGACCTAAACACAGTAGCAGCCGGAACCATGACAG
ACATGTATAAATGTACAGGTGGTCTTTGAGGGATAGCACGAGGTGGTCTGATAGGGCTAACCCTTACCAGCCTCTATGCA
CTATATAATAACTGGGAGCAGATGAATGGCTCCTTGCTCCAACCGTCACTC

Alignment

ORF - retro_cjac_2965 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.51 %
• Parental protein coverage: 59.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTGAAFGAMNGLRLG-LKETQNMAWSKPRNVQILNMVTRQGALWANTLGSLALLYSAFGVIIEKTRGAED
          MT.AAFGA.NGLRL..LKETQNM.WSK.RNVQILNMVTRQGALW.NTLGSLA.L.SAFGVIIEKT.GAED
Retrocopy MTVAAFGALNGLRLD<LKETQNMVWSKSRNVQILNMVTRQGALWTNTLGSLAFLCSAFGVIIEKT*GAED

Parental  DLNTVAAGTMTGMLYKCTGGLRGIARGGLTGLTLTSLYALYNNWEHMKGSLLQQSL
          DLNTVAAGTMT.M.YKCTGGL.GIARGGL.GLTLTSLYALYNNWE.M.GSLLQ.SL
Retrocopy DLNTVAAGTMTDM-YKCTGGL*GIARGGLIGLTLTSLYALYNNWEQMNGSLLQPSL

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	0.02 RPM	11.67 RPM
SRP051959_heart	0.05 RPM	16.38 RPM
SRP051959_kidney	0.04 RPM	19.52 RPM
SRP051959_liver	0.04 RPM	21.27 RPM
SRP051959_lung	0.00 RPM	10.79 RPM
SRP051959_lymph_node	0.00 RPM	10.23 RPM
SRP051959_skeletal_muscle	0.02 RPM	29.52 RPM
SRP051959_spleen	0.00 RPM	11.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2965 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2965 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2965 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007501	1 retrocopy	retro_amel_1488,
Canis familiaris	ENSCAFG00000029477	1 retrocopy	retro_cfam_329,
Choloepus hoffmanni	ENSCHOG00000007073	1 retrocopy	retro_chof_797,
Callithrix jacchus	ENSCJAG00000013336	1 retrocopy	retro_cjac_2965 ,
Cavia porcellus	ENSCPOG00000019917	2 retrocopies	retro_cpor_1013, retro_cpor_321,
Monodelphis domestica	ENSMODG00000002661	2 retrocopies	retro_mdom_1202, retro_mdom_860,
Mus musculus	ENSMUSG00000013701	1 retrocopy	retro_mmus_2,
Oryctolagus cuniculus	ENSOCUG00000000525	1 retrocopy	retro_ocun_73,
Otolemur garnettii	ENSOGAG00000015393	1 retrocopy	retro_ogar_2627,
Ochotona princeps	ENSOPRG00000005255	2 retrocopies	retro_opri_520, retro_opri_920,
Procavia capensis	ENSPCAG00000015914	1 retrocopy	retro_pcap_181,
Rattus norvegicus	ENSRNOG00000019811	3 retrocopies	retro_rnor_1804, retro_rnor_225, retro_rnor_661,
Sorex araneus	ENSSARG00000010335	1 retrocopy	retro_sara_86,
Sus scrofa	ENSSSCG00000025276	1 retrocopy	retro_sscr_404,
Ictidomys tridecemlineatus	ENSSTOG00000007041	1 retrocopy	retro_itri_1043,