RetrogeneDB ID: retro_ecab_218

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:51631489..51631931(+)
• Located in intron of: ENSECAG00000012013

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNB2L1
• Ensembl ID: ENSECAG00000022567
• Aliases: None
• Description: guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1 [Source:RefSeq peptide;Acc:NP_001229375]

Sequence

>retro_ecab_218
ATCAAGCTATGGAATACTCTGGGTGTATACAAATATACTGTCCAGGATGAGAGCTACTCAGAGTGGGTGTCTTGCATCTG
CTTCTCACCAAACAGCAGTATTCCACCATTGTCTCCTGTGGCCGGGACAAGTTGGTCAAGGTGTGGAATTTGGCAAACTG
CAAGCTGAAGGCCAAACACATTGGCCACAGGGGCTACCTGAACACTGTCACTGTCTCTCCAGATGGATCTCTCTGTGCTT
CTGGAGGCAAGGATGGCCAGGCCATGCTTTGAGATTTAAATGAAGAAAAGCACCTTTATACACTAGATGGTGGGGACATC
ATCAACACCTTGTGCTTCAGTCCCAATCGCTACTGGCTCTGTGCTGCCACAGGCCCCAGCATCAAGATCTGGGACTTGAA
GGGCAAGATCATTGTAATGAACTGAAGCAAGAAGTTATCAGT

Alignment

ORF - retro_ecab_218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.67 %
• Parental protein coverage: 98.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IKLWNTLGVCKYTVQDESHSEWVSCVRFSPNSSNP-IIVSCGWDKLVKVWNLANCKLKTNHIGHTGYLNT
          IKLWNTLGV.KYTVQDES.SEWVSC..FSPNSS.P..IVSCG.DKLVKVWNLANCKLK..HIGH.GYLNT
Retrocopy IKLWNTLGVYKYTVQDESYSEWVSCICFSPNSSIP<TIVSCGRDKLVKVWNLANCKLKAKHIGHRGYLNT

Parental  VTVSPDGSLCASGGKDGQAMLWDLNEGKHLYTLDGGDIINALCFSPNRYWLCAATGPSIKIWDLEGKIIV
          VTVSPDGSLCASGGKDGQAML.DLNE.KHLYTLDGGDIIN.LCFSPNRYWLCAATGPSIKIWDL.GKIIV
Retrocopy VTVSPDGSLCASGGKDGQAML*DLNEEKHLYTLDGGDIINTLCFSPNRYWLCAATGPSIKIWDLKGKIIV

Parental  -DELKQEVIS
          ..ELKQEVIS
Retrocopy <NELKQEVIS

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
SRP021940_articular_cartilage	0.59 RPM	699.21 RPM
SRP021940_cerebellum	0.16 RPM	258.05 RPM
SRP021940_embryo	0.56 RPM	518.00 RPM
SRP021940_placental_villous	0.63 RPM	300.94 RPM
SRP021940_synovial_membrane	0.47 RPM	488.51 RPM
SRP021940_testis	0.70 RPM	252.64 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_218 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_218 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_218 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012008	1 retrocopy	retro_acar_185,
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,
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,