RetrogeneDB ID: retro_sscr_1053

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:12148305..12148634(-)
• Located in intron of: ENSSSCG00000014873

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC58
• Ensembl ID: ENSSSCG00000025107
• Aliases: None
• Description: coiled-coil domain containing 58 [Source:HGNC Symbol;Acc:31136]

Sequence

>retro_sscr_1053
CTGGTGGCACCCAGCGGCAGTGTGAACTGTGAGGAGTTCACCAAGTCCCAGGAATTACTCAAGGTGGTGAGGATGAGAGA
TGACAGTATAGTACATGAATTAAACACTGTAGTTCCAACAGCTTCCTTTGCAAGGAAAACTGATGCCAGCCAAACCTGTA
AACAACTTTATGAGTCTCTGATGGAGGCTCATGCCAGCGGGGACAGAGTCATAAAAAACTGTATAGCTCAGACCTCAGTG
GTAGTCAAACAACTTCGAGAAGAGAGAGAAAAGAATTTGGGTGACTTAACGTTATTAAAGCAACTTAGAAAAAACAGGTA
AAATTGAAA

Alignment

ORF - retro_sscr_1053 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.78 %
• Parental protein coverage: 76.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAPSGSVNCEEFAEFQELLKVMRTIDDRIVHELNTTVPTASFAGKIDASQTCKQLYESLMEAHASRDRV
          ..APSGSVNCEEF...QELLKV.R..DD.IVHELNT.VPTASFA.K.DASQTCKQLYESLMEAHAS.DRV
Retrocopy LVAPSGSVNCEEFTKSQELLKVVRMRDDSIVHELNTVVPTASFARKTDASQTCKQLYESLMEAHASGDRV

Parental  IKNCIAQTSAVVKQLREEREKNLDDLTLLKQLR-KEQTKLK
          IKNCIAQTS.VVKQLREEREKNL.DLTLLKQLR.K.Q.KLK
Retrocopy IKNCIAQTSVVVKQLREEREKNLGDLTLLKQLR<KKQVKLK

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
SRP014902_placenta	0.00 RPM	0.53 RPM
SRP014902_testis	0.00 RPM	1.84 RPM
SRP018288_heart	0.00 RPM	12.89 RPM
SRP018288_kidney	0.00 RPM	7.09 RPM
SRP018288_liver	0.00 RPM	8.00 RPM
SRP018288_lung	0.10 RPM	6.92 RPM
SRP018856_adipose	0.00 RPM	4.02 RPM
SRP035408_brain	0.00 RPM	6.45 RPM
SRP035408_liver	0.00 RPM	10.04 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1053 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1053 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1053 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 66 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011138	4 retrocopies	retro_btau_1723, retro_btau_1791, retro_btau_1815, retro_btau_328,
Choloepus hoffmanni	ENSCHOG00000004505	1 retrocopy	retro_chof_1072,
Callithrix jacchus	ENSCJAG00000008132	2 retrocopies	retro_cjac_294, retro_cjac_4115,
Dasypus novemcinctus	ENSDNOG00000005535	1 retrocopy	retro_dnov_743,
Equus caballus	ENSECAG00000023743	2 retrocopies	retro_ecab_1088, retro_ecab_458,
Echinops telfairi	ENSETEG00000003564	3 retrocopies	retro_etel_1361, retro_etel_228, retro_etel_980,
Homo sapiens	ENSG00000160124	3 retrocopies	retro_hsap_1871, retro_hsap_1910, retro_hsap_676,
Gorilla gorilla	ENSGGOG00000001964	9 retrocopies	retro_ggor_132, retro_ggor_1369, retro_ggor_1370, retro_ggor_1939, retro_ggor_2951, retro_ggor_2952, retro_ggor_2953, retro_ggor_582, retro_ggor_722,
Loxodonta africana	ENSLAFG00000016049	1 retrocopy	retro_lafr_227,
Myotis lucifugus	ENSMLUG00000000937	2 retrocopies	retro_mluc_2530, retro_mluc_634,
Macaca mulatta	ENSMMUG00000011919	4 retrocopies	retro_mmul_1104, retro_mmul_2414, retro_mmul_2531, retro_mmul_723,
Monodelphis domestica	ENSMODG00000018298	1 retrocopy	retro_mdom_1936,
Mustela putorius furo	ENSMPUG00000004777	1 retrocopy	retro_mputfur_194,
Mus musculus	ENSMUSG00000075229	1 retrocopy	retro_mmus_1233,
Nomascus leucogenys	ENSNLEG00000000291	6 retrocopies	retro_nleu_1236, retro_nleu_1248, retro_nleu_2697, retro_nleu_390, retro_nleu_435, retro_nleu_683,
Oryctolagus cuniculus	ENSOCUG00000002682	2 retrocopies	retro_ocun_724, retro_ocun_839,
Otolemur garnettii	ENSOGAG00000003190	2 retrocopies	retro_ogar_2498, retro_ogar_817,
Pongo abelii	ENSPPYG00000013486	5 retrocopies	retro_pabe_1551, retro_pabe_3694, retro_pabe_3695, retro_pabe_544, retro_pabe_768,
Pteropus vampyrus	ENSPVAG00000012707	2 retrocopies	retro_pvam_1127, retro_pvam_1318,
Rattus norvegicus	ENSRNOG00000031653	2 retrocopies	retro_rnor_1013, retro_rnor_1576,
Sorex araneus	ENSSARG00000004054	1 retrocopy	retro_sara_596,
Sus scrofa	ENSSSCG00000025107	2 retrocopies	retro_sscr_1053 , retro_sscr_835,
Ictidomys tridecemlineatus	ENSSTOG00000004419	1 retrocopy	retro_itri_247,
Tupaia belangeri	ENSTBEG00000003196	6 retrocopies	retro_tbel_208, retro_tbel_2214, retro_tbel_2781, retro_tbel_2882, retro_tbel_4574, retro_tbel_846,
Tursiops truncatus	ENSTTRG00000013399	1 retrocopy	retro_ttru_72,
Vicugna pacos	ENSVPAG00000002150	1 retrocopy	retro_vpac_445,