RetrogeneDB ID: retro_cjac_2876

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:50167025..50167975(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000008310
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GNB2L1
• Ensembl ID: ENSCJAG00000018752
• Aliases: None
• Description: guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1 [Source:HGNC Symbol;Acc:4399]

Sequence

>retro_cjac_2876
ATGACTGAGCAGATGACTCTTCGTGGCAACCTCAAGGGCCACAACGGCTGGGTAACACAGATTGCTACTACTCCTCAGTT
CCCGGACATGATCCTATCCGCCTCTCAAGACAAGACCATCATCATGTGGAAACTGACCAGGGATGAGACCAACTATGGAA
TTCCACAGCGTGCTCTGCGAGGTCACTCCCACTTTGTTAGTGATGTGGTTATCTCCTCAGATGGCCAGTTTGCCCTCTCA
GGCTCCTGGGATGGAACCCTGCGCCTCTGGGATCTCACAACGGGCACCACCACGAGGCGTTTGTGGGCCATACCAAGGAT
GTGCTGAGTGTGGCGTTCTCCTCTGACAACCGGCAGATTGTCTCTGGATCTCGAGATAAAACCATCAAGCTATGGAATAC
CCTGGGTGTGTGCAAATACACTGTCCAGGATGACAGCCACTCAGAGTGGGTGTCTTGTGTCCGCTTCTCACCCAACAGCA
GCAACCCTATCATTGTCTCCTGCGGCTGGGACAAGCTGGTCAAGGTATGGAACCTGGCTAACTGCAAGCTGAAGACCAAC
CACATTGGCCACACAGGCTATCTGAACACAGTGACTGTCTCTCCAGATGGATCCCTCTGTGCTTCTGGAGGCAAGGATGG
CCAGGCCATGTTATGGGATCTCAACGAAGGCAAGCACCTTTACACCCTAGATGGTGGGGACATCATCAACACCCTATGCT
TCAGCCCTAACCGCTATTGGCTCTGTGCTGCAACAGGCCCCAGCATCAAGATTTGGGATTTAGAGGGGAAGATCATTGTA
GACGAACTGAAGCAGGAAGTTATCAGCACCAGCAGCAAGGCAGAACCACCCCAGTGCACCTCCCTGGCCTGGTCTGCTGA
TGGCCAGACTCTGTTTGCTGGCTATACAGACAACCTGGTGCGAGTGTGGCAGGTGACCACTGGCACCCGC

Alignment

ORF - retro_cjac_2876 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.11 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTEQMTLRGTLKGHNGWVTQIATTPQFPDMILSASRDKTIIMWKLTRDETNYGIPQRALRGHSHFVSDVV
          MTEQMTLRG.LKGHNGWVTQIATTPQFPDMILSAS.DKTIIMWKLTRDETNYGIPQRALRGHSHFVSDVV
Retrocopy MTEQMTLRGNLKGHNGWVTQIATTPQFPDMILSASQDKTIIMWKLTRDETNYGIPQRALRGHSHFVSDVV

Parental  ISSDGQFALSGSWDGTLRLWDLTTGTTTRR-FVGHTKDVLSVAFSSDNRQIVSGSRDKTIKLWNTLGVCK
          ISSDGQFALSGSWDGTLRLWDLTTGTTTRR.FVGHTKDVLSVAFSSDNRQIVSGSRDKTIKLWNTLGVCK
Retrocopy ISSDGQFALSGSWDGTLRLWDLTTGTTTRR<FVGHTKDVLSVAFSSDNRQIVSGSRDKTIKLWNTLGVCK

Parental  YTVQDESHSEWVSCVRFSPNSSNPIIVSCGWDKLVKVWNLANCKLKTNHIGHTGYLNTVTVSPDGSLCAS
          YTVQD.SHSEWVSCVRFSPNSSNPIIVSCGWDKLVKVWNLANCKLKTNHIGHTGYLNTVTVSPDGSLCAS
Retrocopy YTVQDDSHSEWVSCVRFSPNSSNPIIVSCGWDKLVKVWNLANCKLKTNHIGHTGYLNTVTVSPDGSLCAS

Parental  GGKDGQAMLWDLNEGKHLYTLDGGDIINALCFSPNRYWLCAATGPSIKIWDLEGKIIVDELKQEVISTSS
          GGKDGQAMLWDLNEGKHLYTLDGGDIIN.LCFSPNRYWLCAATGPSIKIWDLEGKIIVDELKQEVISTSS
Retrocopy GGKDGQAMLWDLNEGKHLYTLDGGDIINTLCFSPNRYWLCAATGPSIKIWDLEGKIIVDELKQEVISTSS

Parental  KAEPPQCTSLAWSADGQTLFAGYTDNLVRVWQVTIGTR
          KAEPPQCTSLAWSADGQTLFAGYTDNLVRVWQVT.GTR
Retrocopy KAEPPQCTSLAWSADGQTLFAGYTDNLVRVWQVTTGTR

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	0.64 RPM	150.32 RPM
SRP051959_heart	0.47 RPM	107.00 RPM
SRP051959_kidney	1.11 RPM	143.57 RPM
SRP051959_liver	0.84 RPM	194.64 RPM
SRP051959_lung	1.04 RPM	134.21 RPM
SRP051959_lymph_node	1.05 RPM	191.29 RPM
SRP051959_skeletal_muscle	1.07 RPM	166.34 RPM
SRP051959_spleen	0.74 RPM	174.48 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2876 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2876 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2876 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012008	1 retrocopy	retro_acar_185,
Ailuropoda melanoleuca	ENSAMEG00000000004	1 retrocopy	retro_amel_1627,
Bos taurus	ENSBTAG00000019648	1 retrocopy	retro_btau_1461,
Canis familiaris	ENSCAFG00000024818	1 retrocopy	retro_cfam_1824,
Callithrix jacchus	ENSCJAG00000018752	1 retrocopy	retro_cjac_2876 ,
Cavia porcellus	ENSCPOG00000008724	1 retrocopy	retro_cpor_687,
Dipodomys ordii	ENSDORG00000010735	1 retrocopy	retro_dord_117,
Equus caballus	ENSECAG00000022567	3 retrocopies	retro_ecab_172, retro_ecab_218, retro_ecab_986,
Erinaceus europaeus	ENSEEUG00000008729	1 retrocopy	retro_eeur_368,
Echinops telfairi	ENSETEG00000016024	3 retrocopies	retro_etel_1135, retro_etel_114, retro_etel_2086,
Homo sapiens	ENSG00000204628	1 retrocopy	retro_hsap_3226,
Gorilla gorilla	ENSGGOG00000025367	1 retrocopy	retro_ggor_2194,
Macropus eugenii	ENSMEUG00000011055	3 retrocopies	retro_meug_1095, retro_meug_1109, retro_meug_1532,
Myotis lucifugus	ENSMLUG00000015507	1 retrocopy	retro_mluc_811,
Macaca mulatta	ENSMMUG00000003604	1 retrocopy	retro_mmul_1956,
Monodelphis domestica	ENSMODG00000004091	1 retrocopy	retro_mdom_1426,
Mustela putorius furo	ENSMPUG00000001148	2 retrocopies	retro_mputfur_1103, retro_mputfur_1111,
Mus musculus	ENSMUSG00000020372	1 retrocopy	retro_mmus_3282,
Nomascus leucogenys	ENSNLEG00000002604	1 retrocopy	retro_nleu_729,
Ornithorhynchus anatinus	ENSOANG00000002600	1 retrocopy	retro_oana_127,
Otolemur garnettii	ENSOGAG00000014924	2 retrocopies	retro_ogar_1257, retro_ogar_1591,
Pongo abelii	ENSPPYG00000019939	1 retrocopy	retro_pabe_149,
Pan troglodytes	ENSPTRG00000022734	1 retrocopy	retro_ptro_2178,
Rattus norvegicus	ENSRNOG00000002390	3 retrocopies	retro_rnor_1831, retro_rnor_2130, retro_rnor_895,
Ictidomys tridecemlineatus	ENSSTOG00000007063	1 retrocopy	retro_itri_1752,
Tupaia belangeri	ENSTBEG00000014661	2 retrocopies	retro_tbel_3897, retro_tbel_3899,