RetrogeneDB ID: retro_sscr_688

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:149143257..149144157(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000027249
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000009373
• Aliases: None
• Description: Sus scrofa solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 15 (SLC25A15), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001243910]

Sequence

>retro_sscr_688
ATGAATTGCAGTCCTGCCCTGCAAGCCGCCATCGACCTGACCGCGGGGGCCCTCGGGGGCACAGCGTGCGTCCTGACCGG
GCAGCCCTTCGACACGATGAAAGTGAAGATGCAGACGTTCCCCGGTCTCTACAAGGGCCTCGCCGACTGCGGCCTCAAGA
CCTACGCCCAGGTGGGCCTGCGGGGCTTCTACAAGGGGACCGGCCCCGCGCTGATGGCCTGCGTCGCCGAGAACTCGGTC
CTCTTTATGTGCTACGGCTTCTGCCAACAGTTCGTCAGGAAAGTGGTTGGACTGGACCAGCAGGAGAAGCTGAGGGATCT
GCAGACGGCGGCCGCCGGTTCCTCCGCCTCCGCCTTTGCCGCGCTGGCCCTGTGCCCCACGGAGCTTGTCAAGTGCCAGC
TGCAGACCATGCTCGAACTGGAGATGTCAGGGAGGCTGGCAAAAAGCCCTAAGACGGTTTGGGGCGTCGTGAAGAGCATC
CTTCGAAAGGATGGGCCCTTGGGCTTCTCCCACGGACTCTGGAGCACTCTGCTTCAAGAAGTGCCGGGCTATTTCTTCTT
CTTCGGTGGCTATGAACTGAGCCGATCGTTTTTTGCGTCCGGGGGATCAAAAGATGAACTAGGCCCTGTCCCCTTGATGT
TAAGTGGTGGAATTGCTGGAATTTGCCTTTGGCTTGTCATATACCCTGTGGATTGTGTCAAATCCAGAATTCAGGTTCTT
TCCATGTTTGGAAAGCAGGCAGGATTTATGGGAACTCTTTTAAGTGTTGTGAAAAATGAAGGAATAGCAGCCTTATATTC
TGGAATGAAAGCTACTTTGATTCGAGCCTTCCCTGCCAATGGGTCACTGTTTTTGGCTTATGAATACAGCAGGAAGTTGA
TGATGAGCCAGTTTGAAGCA

Alignment

ORF - retro_sscr_688 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 99.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKSNPAIQAAIDLTAGAAGGTACVLTGQPFDTMKVKMQTFPDLYRGLTDCCLKTYSQVGFRGFYKGTSPA
          M...PA.QAAIDLTAGA.GGTACVLTGQPFDTMKVKMQTFP.LY.GL.DC.LKTY.QVG.RGFYKGT.PA
Retrocopy MNCSPALQAAIDLTAGALGGTACVLTGQPFDTMKVKMQTFPGLYKGLADCGLKTYAQVGLRGFYKGTGPA

Parental  LIANIAENSVLFMCYGFCQQVVRKVAGLDRQAKLSDLQNAAAGSFASAFAALVLCPTELVKCRLQTMYEM
          L.A..AENSVLFMCYGFCQQ.VRKV.GLD.Q.KL.DLQ.AAAGS.ASAFAAL.LCPTELVKC.LQTM.E.
Retrocopy LMACVAENSVLFMCYGFCQQFVRKVVGLDQQEKLRDLQTAAAGSSASAFAALALCPTELVKCQLQTMLEL

Parental  ETSGKIAKSQNTVWSVVKSILRKDGPLGFYHGLSSTLLREVPGYFFFFGGYELSRSFFASGRSKDELGPV
          E.SG..AKS..TVW.VVKSILRKDGPLGF.HGL.STLL.EVPGYFFFFGGYELSRSFFASG.SKDELGPV
Retrocopy EMSGRLAKSPKTVWGVVKSILRKDGPLGFSHGLWSTLLQEVPGYFFFFGGYELSRSFFASGGSKDELGPV

Parental  PLMLSGGFGGICLWLAVYPVDCIKSRIQVLSMSGKQAGFIGTFISVVKNEGITALYSGLKPTMIRAFPAN
          PLMLSGG..GICLWL..YPVDC.KSRIQVLSM.GKQAGF.GT..SVVKNEGI.ALYSG.K.T.IRAFPAN
Retrocopy PLMLSGGIAGICLWLVIYPVDCVKSRIQVLSMFGKQAGFMGTLLSVVKNEGIAALYSGMKATLIRAFPAN

Parental  GALFLAYEYSRKLMMSQFEA
          G.LFLAYEYSRKLMMSQFEA
Retrocopy GSLFLAYEYSRKLMMSQFEA

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	0.80 RPM	5.84 RPM
SRP014902_testis	0.42 RPM	14.57 RPM
SRP018288_heart	0.03 RPM	9.06 RPM
SRP018288_kidney	0.10 RPM	174.16 RPM
SRP018288_liver	0.16 RPM	222.75 RPM
SRP018288_lung	0.10 RPM	4.17 RPM
SRP018856_adipose	0.38 RPM	5.77 RPM
SRP035408_brain	0.00 RPM	5.62 RPM
SRP035408_liver	0.00 RPM	215.50 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_688 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_688 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_688 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_1581

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011723	1 retrocopy	retro_amel_5,
Bos taurus	ENSBTAG00000011647	1 retrocopy	retro_btau_1581,
Canis familiaris	ENSCAFG00000005955	1 retrocopy	retro_cfam_211,
Choloepus hoffmanni	ENSCHOG00000004899	3 retrocopies	retro_chof_1643, retro_chof_494, retro_chof_561,
Erinaceus europaeus	ENSEEUG00000014870	1 retrocopy	retro_eeur_329,
Mus musculus	ENSMUSG00000031482	1 retrocopy	retro_mmus_75,
Oryctolagus cuniculus	ENSOCUG00000016684	2 retrocopies	retro_ocun_192, retro_ocun_1927,
Ochotona princeps	ENSOPRG00000014616	1 retrocopy	retro_opri_7,
Rattus norvegicus	ENSRNOG00000011881	1 retrocopy	retro_rnor_130,
Sorex araneus	ENSSARG00000002472	1 retrocopy	retro_sara_30,
Sus scrofa	ENSSSCG00000009373	1 retrocopy	retro_sscr_688 ,