RetrogeneDB ID: retro_sscr_858

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:16833370..16833632(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCEB2
• Ensembl ID: ENSSSCG00000008061
• Aliases: None
• Description: transcription elongation factor B (SIII), polypeptide 2 (18kDa, elongin B) [Source:HGNC Symbol;Acc:11619]

Sequence

>retro_sscr_858
ACCATCTTCAGGGACGCTAAGGAGTCAAGCACAGTGCTAGGGATGAAGCGCCTTGTGAAAAGGCATTCTCAGGTGGCCAC
CAGCACAAGGAGCAGCTTTACAAAGATGACCAGCTCCTGGACAAGAGCATGACCCTGGAGGAGTGTGGCTACACCCGGTG
GACACCCCTGTCCACCCGCCGTTCACCCTGGACCTGGGTCTTCCTGCAGATAGGGCCCATCTGGCGTTTGACACCCTTAG
CCTGAAGCCCTTCTTCAACCCA

Alignment

ORF - retro_sscr_858 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.11 %
• Parental protein coverage: 71.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TIFTDAKESSTVFELKRIVE-GILKRPPDE-QRLYKDDQLLDDGKTLGECGFTSQT-ARPQAPATVGLAF
          TIF.DAKESSTV...KR.V..GIL..PP.....LYKDDQLLD...TL.ECG.T..T......P.T..L..
Retrocopy TIFRDAKESSTVLGMKRLVK>GILRWPPAQ>EQLYKDDQLLDKSMTLEECGYTRWT<TPVHPPFTLDLGL

Parental  RADEA---FEALRIEPFSSP
          .AD.A...F..L...PF..P
Retrocopy PADRAHLAFDTLSLKPFFNP

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	104.06 RPM
SRP014902_testis	0.00 RPM	144.42 RPM
SRP018288_heart	0.00 RPM	53.12 RPM
SRP018288_kidney	0.00 RPM	81.07 RPM
SRP018288_liver	0.00 RPM	55.49 RPM
SRP018288_lung	0.00 RPM	73.11 RPM
SRP018856_adipose	0.00 RPM	78.89 RPM
SRP035408_brain	0.00 RPM	99.98 RPM
SRP035408_liver	0.00 RPM	74.80 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_858 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_858 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_858 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019543	3 retrocopies	retro_btau_142, retro_btau_17, retro_btau_29,
Callithrix jacchus	ENSCJAG00000015347	10 retrocopies	retro_cjac_1593, retro_cjac_1606, retro_cjac_2051, retro_cjac_2613, retro_cjac_2987, retro_cjac_3030, retro_cjac_342, retro_cjac_3819, retro_cjac_639, retro_cjac_959,
Cavia porcellus	ENSCPOG00000021024	1 retrocopy	retro_cpor_1416,
Felis catus	ENSFCAG00000004711	2 retrocopies	retro_fcat_112, retro_fcat_40,
Homo sapiens	ENSG00000103363	2 retrocopies	retro_hsap_1246, retro_hsap_940,
Gorilla gorilla	ENSGGOG00000015306	1 retrocopy	retro_ggor_976,
Monodelphis domestica	ENSMODG00000016536	4 retrocopies	retro_mdom_1149, retro_mdom_1617, retro_mdom_1964, retro_mdom_23,
Mus musculus	ENSMUSG00000055839	7 retrocopies	retro_mmus_1212, retro_mmus_1489, retro_mmus_1664, retro_mmus_2930, retro_mmus_511, retro_mmus_747, retro_mmus_99,
Nomascus leucogenys	ENSNLEG00000009471	2 retrocopies	retro_nleu_295, retro_nleu_89,
Oryctolagus cuniculus	ENSOCUG00000010116	2 retrocopies	retro_ocun_202, retro_ocun_930,
Pongo abelii	ENSPPYG00000007013	1 retrocopy	retro_pabe_74,
Pan troglodytes	ENSPTRG00000007663	1 retrocopy	retro_ptro_857,
Rattus norvegicus	ENSRNOG00000004814	6 retrocopies	retro_rnor_1226, retro_rnor_1275, retro_rnor_185, retro_rnor_1948, retro_rnor_35, retro_rnor_352,
Sus scrofa	ENSSSCG00000008061	1 retrocopy	retro_sscr_858 ,