RetrogeneDB ID: retro_sscr_770

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 4:18955234..18956316(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD23B
• Ensembl ID: ENSSSCG00000005436
• Aliases: None
• Description: RAD23 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:9813]

Sequence

>retro_sscr_770
TTAATTTTTGCAGGCAAAATCCTCAATGACGATACTGCTCTAAAAGAATATAAAATTGATGAGAAAAATTTCGTGGTTGT
TATGGTGACAAAACCCAAAGGAGTGACAACAGAAGCACCAGCTACACCTCAGCAGTCAAATTCTTCCACCACTACCACAG
TTAGTTAGTTCCTCCACAGCACCAACTGTGGCTAAGGCCCCAAACCTGCCCCTGTTTTGGCTCCTACTCCCATACCTTCA
TCCATCATCCCAGCATCAACGACAGCATCTTCTGAACTTGCACCTGCTAGTGCAATGAAACAGGAGAAACCTGAGGAAAG
GCCGGTGGAAACACCAGCGACTACTAGCCCATGACAGTACATCAGGAGATTCTTCCCAATCAAATCTTTTTGAAGATGCA
AAAAGTGCTCTTGTGACAGGTCAGTCGTACGAGAATATGGTAACTGAGATCATGTCAATGGGTTATGAACGAGAGCAAGT
AATTGCAGCCCTGAGAGCCAATTTCAACAACCCTGAACAAAGCAGTGGAATATCTTTTAATGGGAATTCCTGGATATTGA
GAAAGTCGGGCCGTGGTTGACCCCCTCCAGCAGCTAGTACTGGGGTTCCTCAGTCTTCAGTGACTGCAGCTGCAGCAACT
GTGACAGCAATGACAATAACAAAAAGTTCCAGAGGACAGCCTCTTGAATTTTTACAGAATCAGCCCCAGTTTCAACAGAT
GAGACAAATTATTCAACAGAATCCCTGCCTGCTTCCAGCAATGCTACAACAGATAGGTGAGAAAATCCTCAGTTGCTGCA
GCAAATTATCCAACACCAGCAACATTTTATTCAGATGTTAAGTGAACCAGTTCAAAAAGCTGGTGGTCAAGGAGGAGGGG
GTGGAGGTGGTAATGGAGGAATTGCAGAAGCTGAAAGTGGTCATAAGAACGACATTCAAGTAACACCTCAGGAAAAAGAA
GCTATGGAAAGGTTAAAGGCGTTAGGATTTCCTGAAGGACTTGTGATGCAAGCATATTTTGCTTGTGAGAGAATGAGAAC
TTGGCTGCCAATTTAATTCTACAGCAAAACTTTGTTGAAGAC

Alignment

ORF - retro_sscr_770 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.18 %
• Parental protein coverage: 88.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  LIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKAVTTPAPATTQQSNSAT-TTT-VSSSTAPAAAQAPT-
          LI.AGKILNDDTALKEYKIDEKNFVVVMVTKPK.VTT.APAT.QQSNS.T.TT..VSSSTAP..A.AP..
Retrocopy LIFAGKILNDDTALKEYKIDEKNFVVVMVTKPKGVTTEAPATPQQSNSSTTTTV>VSSSTAPTVAKAPN<

Parental  PAPALAPTPTPASITPASTTASSEPAPASATKQEKPAEKPAETPVAT-SPTST-DSTSGDSSRSNLFEDA
          PAP.LAPTP.P.SI.PASTTASSE.APASA.KQ....EKP.E.PV.T...TS..DSTSGDSS.SNLFEDA
Retrocopy PAPVLAPTPIPSSIIPASTTASSELAPASAMKQ----EKPEERPVETPATTSP>DSTSGDSSQSNLFEDA

Parental  TSALVTGQSYENMVTEIMSMGYEREQVIAALRASFNNPD-RAVEYLLMGIPGDRESQAVVDP-PPAASTG
          .SALVTGQSYENMVTEIMSMGYEREQVIAALRA.FNNP...AVEYLLMGIPG..ES.AVVDP.PPAASTG
Retrocopy KSALVTGQSYENMVTEIMSMGYEREQVIAALRANFNNPE>KAVEYLLMGIPGY*ESRAVVDP<PPAASTG

Parental  APQSSVAAAAATTTATTTTTSSGGHPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGR-ENPQLLQQIS
          .PQSSV.AAAAT.TA.T.T.SS.G.PLEFL.NQPQFQQMRQIIQQNP.LLPA.LQQIG..ENPQLLQQI.
Retrocopy VPQSSVTAAAATVTAMTITKSSRGQPLEFLQNQPQFQQMRQIIQQNPCLLPAMLQQIGE<ENPQLLQQII

Parental  QHQEHFIQMLNEPVQEAGSQGGGGGGGSGGIAEAGSGHMNYIQVTPQEKEAIERLKALGFPEGLVIQAYF
          QHQ.HFIQML.EPVQ.AG.QGGGGGGG.GGIAEA.SGH.N.IQVTPQEKEA.ERLKALGFPEGLV.QAYF
Retrocopy QHQQHFIQMLSEPVQKAGGQGGGGGGGNGGIAEAESGHKNDIQVTPQEKEAMERLKALGFPEGLVMQAYF

Parental  ACEK-NENLAANFLLQQNFDED
          ACE..NENLAAN..LQQNF.ED
Retrocopy ACER<NENLAANLILQQNFVED

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	74.73 RPM
SRP014902_testis	0.14 RPM	94.34 RPM
SRP018288_heart	0.00 RPM	107.00 RPM
SRP018288_kidney	0.00 RPM	123.72 RPM
SRP018288_liver	0.00 RPM	178.46 RPM
SRP018288_lung	0.00 RPM	187.97 RPM
SRP018856_adipose	0.00 RPM	79.78 RPM
SRP035408_brain	0.00 RPM	135.05 RPM
SRP035408_liver	0.00 RPM	102.54 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_770 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_770 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_770 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001926	1 retrocopy	retro_btau_877,
Callithrix jacchus	ENSCJAG00000016908	2 retrocopies	retro_cjac_3865, retro_cjac_4184,
Dasypus novemcinctus	ENSDNOG00000001174	2 retrocopies	retro_dnov_1982, retro_dnov_989,
Equus caballus	ENSECAG00000021928	1 retrocopy	retro_ecab_361,
Homo sapiens	ENSG00000119318	2 retrocopies	retro_hsap_2611, retro_hsap_3754,
Gorilla gorilla	ENSGGOG00000002511	1 retrocopy	retro_ggor_1829,
Loxodonta africana	ENSLAFG00000007533	1 retrocopy	retro_lafr_1109,
Macaca mulatta	ENSMMUG00000014944	2 retrocopies	retro_mmul_1476, retro_mmul_1725,
Nomascus leucogenys	ENSNLEG00000017319	1 retrocopy	retro_nleu_1590,
Oryctolagus cuniculus	ENSOCUG00000007316	1 retrocopy	retro_ocun_1429,
Otolemur garnettii	ENSOGAG00000014216	1 retrocopy	retro_ogar_3040,
Pongo abelii	ENSPPYG00000019477	2 retrocopies	retro_pabe_2344, retro_pabe_3162,
Pan troglodytes	ENSPTRG00000021229	1 retrocopy	retro_ptro_1760,
Sarcophilus harrisii	ENSSHAG00000011925	1 retrocopy	retro_shar_248,
Sus scrofa	ENSSSCG00000005436	1 retrocopy	retro_sscr_770 ,
Tursiops truncatus	ENSTTRG00000007597	1 retrocopy	retro_ttru_1401,