RetrogeneDB ID: retro_sscr_507

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:104794961..104796316(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM91A1
• Ensembl ID: ENSSSCG00000024424
• Aliases: None
• Description: family with sequence similarity 91, member A1 [Source:HGNC Symbol;Acc:26306]

Sequence

>retro_sscr_507
ACTGCCTTTTCAATGATGGGAAATCTTTCACCAAACTTGAAAAGCCATGCAGTCACAATGTTTGAAGTTGGCAAACTCTC
AGAAGAGTCTCTGGACAGCTTTCTTATAGAACTAGAAAAGGTTTAAAGCACTGGTGAAGGAGAAGCACAGAGATATTTTG
ATCATGCACTTACTCTGAGAAACACAATATTGTTTCTGCGTCATAATAAAGATCTAGTTGCACAAACTGCACAGCCAGAC
CAACCCAATTATGGTTTTTCTCTGGATCTCTTGCACTGTGAAAGCCTTCTGGGATTGGACCCTGCAACTTGCAGCAGAGT
TCTAAACAAAAATTACACCCTGCTTGTCTCCATGGCTCCTCTTACCAATGAAATACGGCCTGTCAGCAGCTGCACACCTC
AGCATATTGGACCAGCTATCCCAGCAGTCAGTTCTGTCTGGTTTAAGCTGTACATTTACTATATCACCAGGCAAGGACCA
CCATCTCTTTTACTGTCCTAAGATACAAGACTTCGAAAACTGCCAGATATGTTCCAGGGTTTTGATCAATTACTAATAAC
GTTACGGAGTCATGATCCTGAGGTGGTTTCTACATCAAATGTGCTCACAATGTTGAATGATGCTTTAACACTTTCAGCAG
TTTTGATTCAGGGACATGGTCTGCATGTGATAGGAGAAACTGTCCACATACCTTTCCTGTTTGATGAGACAGAACTCCAA
GGAGAGTTTACTTGTGTTAATATGGGTGTCCATAAAGCAGTGCAAATATTAAGGAACAAAGTGGACTTGCAGCATTTTTG
TGGATATGTCACCATGTTGAATGCTTCTAGCCAGCTTGCAAACAGAAAACTCAGTGATGTTTATGACGAGAGAGGAGAAC
CTGATTTGGCTTCTAGCTCAGATGTAAATGGGAGTACAGAGTCATTTGAAATGGTCGTTGAGGAAGCAGTGTAGACTCAG
CCACAAAGCAAAACTCTGTTGCCACAACAGAAGCAGATTGGGTTCTTCTCGAGCTGTGCTTTGGAATTCCACTATTTAGT
TCTGAATTAAATCAGAAAGTTTGCAGAAAAGATTGCTACTCATGGCCTTTGCAGAAAAGAGAGCCTTCAAAACCTCTTGC
ATTCCAGTAGAAAACTGTCTCTACAAGTCCTTAACTTTGTTCACTCATTCCAGGAAGCTGCTTCACCACTGGATATCCAC
AATGAAGCCAGTTTTTCAGGTTTGCTTCCACAGTCATCCTGTGCCGACGCAGAGTTCCACTTCCTGCAAAAAACTTAATA
TTTAAAGATGGAATCTTAACAGAATGGAGCGGATGGTCACCTTCCTTGCTTCTTCTTGCTAATCTCCATATGCAA

Alignment

ORF - retro_sscr_507 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.43 %
• Parental protein coverage: 53.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TAFLMMGNLSPNLKSHAVTMFEVGKLSDESLDSFLIELEKVQSTGEGEAQRYFDHALTLRNTILFLRHNK
          TAF.MMGNLSPNLKSHAVTMFEVGKLS.ESLDSFLIELEKV.STGEGEAQRYFDHALTLRNTILFLRHNK
Retrocopy TAFSMMGNLSPNLKSHAVTMFEVGKLSEESLDSFLIELEKV*STGEGEAQRYFDHALTLRNTILFLRHNK

Parental  DLVAQTAQPDQPNYGFPLDLLRCESLLGLDPATCSRVLNKNYTLLVSMAPLTNEIRPVSSCTPQHIGPAI
          DLVAQTAQPDQPNYGF.LDLL.CESLLGLDPATCSRVLNKNYTLLVSMAPLTNEIRPVSSCTPQHIGPAI
Retrocopy DLVAQTAQPDQPNYGFSLDLLHCESLLGLDPATCSRVLNKNYTLLVSMAPLTNEIRPVSSCTPQHIGPAI

Parental  PEVSSVWFKLYIYHITRQGPPSLLLSKGTRLRKLPDIFQGYDRLLITSWGHDPGVVPTSNVLTMLNDALT
          P.VSSVWFKLYIY.ITRQGPPSLLLS..TRLRKLPD.FQG.D.LLIT...HDP.VV.TSNVLTMLNDALT
Retrocopy PAVSSVWFKLYIYYITRQGPPSLLLS*DTRLRKLPDMFQGFDQLLITLRSHDPEVVSTSNVLTMLNDALT

Parental  HSAVLIQGHGLHGIGETVHIPFPFDETELQGEFTRVNMGVHKALQILRSKVDLQHFCGYVTMLNASSQLA
          .SAVLIQGHGLH.IGETVHIPF.FDETELQGEFT.VNMGVHKA.QILR.KVDLQHFCGYVTMLNASSQLA
Retrocopy LSAVLIQGHGLHVIGETVHIPFLFDETELQGEFTCVNMGVHKAVQILRNKVDLQHFCGYVTMLNASSQLA

Parental  NRKLSDASDERGEPDLASGSDVNGSTESFEMVIEEA-AVDSATKQNSVATTEADWVPLELCFGIPLFSSE
          NRKLSD..DERGEPDLAS.SDVNGSTESFEMV.EEA..VDSATKQNSVATTEADWV.LELCFGIPLFSSE
Retrocopy NRKLSDVYDERGEPDLASSSDVNGSTESFEMVVEEA<SVDSATKQNSVATTEADWVLLELCFGIPLFSSE

Parental  LNQKVCR-KIATHGLCRKESLQNLLHSSRKLSLQVLNFVHSFQESASPLDIHTEASFSGLLSQSSCADV-
          LNQKVCR.KIATHGLCRKESLQNLLHSSRKLSLQVLNFVHSFQE.ASPLDIH.EASFSGLL.QSSCAD..
Retrocopy LNQKVCR>KIATHGLCRKESLQNLLHSSRKLSLQVLNFVHSFQEAASPLDIHNEASFSGLLPQSSCADA<

Parental  GVPLPAKNLIFKDGILTEWSGRSPSSLLLANLHMQ
          .VPLPAKNLIFKDGILTEWSG.SPS.LLLANLHMQ
Retrocopy RVPLPAKNLIFKDGILTEWSGWSPSLLLLANLHMQ

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	23.10 RPM
SRP014902_testis	0.00 RPM	44.13 RPM
SRP018288_heart	0.00 RPM	34.16 RPM
SRP018288_kidney	0.00 RPM	69.05 RPM
SRP018288_liver	0.00 RPM	62.36 RPM
SRP018288_lung	0.00 RPM	64.97 RPM
SRP018856_adipose	0.00 RPM	31.16 RPM
SRP035408_brain	0.00 RPM	15.02 RPM
SRP035408_liver	0.00 RPM	17.79 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_507 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_507 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_507 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000176853	2 retrocopies	retro_hsap_225, retro_hsap_226,
Nomascus leucogenys	ENSNLEG00000005385	1 retrocopy	retro_nleu_3035,
Sus scrofa	ENSSSCG00000024424	2 retrocopies	retro_sscr_470, retro_sscr_507 ,
Tarsius syrichta	ENSTSYG00000004376	1 retrocopy	retro_tsyr_342,