RetrogeneDB ID: retro_sscr_404

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:14203689..14204231(+)
• Located in intron of: ENSSSCG00000009683

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000025276
• Aliases: None
• Description: None

Sequence

>retro_sscr_404
GCGGGTCTGGTGGTAGTCTTGCTAACTGGTATGAACCCTCTATCTCCTTATTTAAATGTGGATCCATGATATCTTGTGCA
GGACACAGATGAGTGTATTTTGCTAACTGGAGCTAATAAAACCTGGGGCAGACTTGAACTGGCCTTCTTTACCACTGGAG
GATGTTGTAAGACAGGGGCTGCATTTGTAGTTGTAAATGGCCTACGGCTAGGATTGAAGGAAACCCAGAACAGGTCTGGT
CCAAACCAAGAAACATACAGATTTTGAATATGATGACTAGGCAAGGGGCACTTTGGGCTAATACTGTAGGTTCTCTGGCT
TTGCTCTATAGTGCATTTGCTGTCATCATTGAGAAAACTAGAGGTGCAGAAGATGACCACAACACAGTAGCAACTGGAAC
CATGACAGGCATGTTATATAAATGTACAGGTGGTCTTCGAGGGGTAGCACGAGGTAGTCTAGCAGGACTAACACTTATAA
GCCTCTATGCACTATATAATAACTGGGAGTACATGAAAGGCTCCTTATTGCAACAGTCACTC

Alignment

ORF - retro_sscr_404 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.26 %
• Parental protein coverage: 86.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ADLAGVPLTGMNPLSPYLNVDPRYLVQDTDEFILPTGANKTRGRFELAFFTIGGCCMTGAAFGAVNGLRL
          A.L..V.LTGMNPLSPYLNVDP.YLVQDTDE.IL.TGANKT.GR.ELAFFT.GGCC.TGAAF..VNGLRL
Retrocopy AGLVVVLLTGMNPLSPYLNVDP*YLVQDTDECILLTGANKTWGRLELAFFTTGGCCKTGAAFVVVNGLRL

Parental  GLKETQNMA-WSKPRNVQILNMVTRQGALWANTLGSLALLYSAFGVIIEKTRGAEDDLNTVAAGTMTGML
          GLKETQN...WSKPRN.QILNM.TRQGALWANT.GSLALLYSAF.VIIEKTRGAEDD.NTVA.GTMTGML
Retrocopy GLKETQNRS<WSKPRNIQILNMMTRQGALWANTVGSLALLYSAFAVIIEKTRGAEDDHNTVATGTMTGML

Parental  YKCTGGLRGVARGGLAGLTLTSLYALYNNWEHMKGSLLQQSL
          YKCTGGLRGVARG.LAGLTL.SLYALYNNWE.MKGSLLQQSL
Retrocopy YKCTGGLRGVARGSLAGLTLISLYALYNNWEYMKGSLLQQSL

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	0.13 RPM	7.83 RPM
SRP014902_testis	0.00 RPM	16.55 RPM
SRP018288_heart	0.00 RPM	51.44 RPM
SRP018288_kidney	0.00 RPM	62.45 RPM
SRP018288_liver	0.00 RPM	44.45 RPM
SRP018288_lung	0.10 RPM	29.84 RPM
SRP018856_adipose	0.02 RPM	23.61 RPM
SRP035408_brain	0.00 RPM	29.44 RPM
SRP035408_liver	0.00 RPM	25.57 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_404 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_404 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_404 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,