RetrogeneDB ID: retro_sscr_11

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:147054500..147055250(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000015620
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000010685
• Aliases: None
• Description: None

Sequence

>retro_sscr_11
ATGGATGCGCGAGTAGTTAAAGATATGGCAACTGGAAAATCCAAAGGCTATGGCTCTGTATCTTTCTTTTACAACAAACT
GGATGCAGAAAATGCAATTGTGCGTATGGGAGGTCAGTGGTTGGGTGGTCGTCAAATCAAAACCAGTTGGGCCACACGTA
AACCACCTGCACCTAAAAGTACACAAGAAAATAACACTAAGCAGTTGAAATTTGAAGATGTAGTAAACCAGTCAAGTTCA
AAAAATTGTACTGTGTACTGCGGAGGAATTGCTTCTGGGTTAACAGATCAGCTTATGAGACAGACATTCTCACCATTTGG
GCAAATTATGGAAATCAGAGTTTTTCCGGAGAAGCGCTATTCATTTGTCAGATTTTCCACCCATGGAAGTGCAGCCCATG
CCATTGTCTCAGTGACTGGTACTACGATCGAAGGACGTGTTGTTAAATGCTATTGGGGTAAAGAATCTCCTGATATGACT
GAAAACTATAGTCGGTGGGGCCAGTGGAGCCAAGTTTATGGAGATCCACAAGAGCATGGGGATTTGAGTCCAGTGGCAAA
TGGGTGGCAAGTACCACCTGACAGAGTATACGGGCAGCCATGGAATCAGCGAGGATTTGGAGTAGATCAATCACCTTCAG
CTGCTTGCCTGGGTGGATTTGGTGCTCAGCCTCCCCAAGGACAAGCCCCTCCCCCTGTAATACCTCCTCCCAACCAGGCT
GGATACGGCATGGCCAGTTACCGAACACAG

Alignment

ORF - retro_sscr_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.83 %
• Parental protein coverage: 64.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DARVVKDMATGKSKGYGFVSF-YNKLDAENAIVHMGGQWLGGRQIRTNWATRKPPAPKSTQENNTKQLRF
          DARVVKDMATGKSKGYG.VSF.YNKLDAENAIV.MGGQWLGGRQI.T.WATRKPPAPKSTQENNTKQL.F
Retrocopy DARVVKDMATGKSKGYGSVSFFYNKLDAENAIVRMGGQWLGGRQIKTSWATRKPPAPKSTQENNTKQLKF

Parental  EDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGT
          EDVVNQSS.KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK.YSFVRFSTH.SAAHAIVSV.GT
Retrocopy EDVVNQSSSKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKRYSFVRFSTHGSAAHAIVSVTGT

Parental  TIEGHVVKCYWGKESPDMTKNFQQVDYSQWGQWSQVYGNPQQYGQY--MANGWQVPPYGVYGQPWNQQGF
          TIEG.VVKCYWGKESPDMT.N.......QW...SQVYG.PQ..G.....ANGWQVPP..VYGQPWNQ.GF
Retrocopy TIEGRVVKCYWGKESPDMTENYSR--WGQW---SQVYGDPQEHGDLSPVANGWQVPPDRVYGQPWNQRGF

Parental  GVDQSPSAAWMGGFGAQPPQGQAPPPVIPPPNQAGYGMASYQTQ
          GVDQSPSAA..GGFGAQPPQGQAPPPVIPPPNQAGYGMASY.TQ
Retrocopy GVDQSPSAACLGGFGAQPPQGQAPPPVIPPPNQAGYGMASYRTQ

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	0.27 RPM	37.43 RPM
SRP014902_testis	0.00 RPM	66.06 RPM
SRP018288_heart	0.00 RPM	62.29 RPM
SRP018288_kidney	0.20 RPM	61.57 RPM
SRP018288_liver	0.32 RPM	55.65 RPM
SRP018288_lung	0.00 RPM	63.84 RPM
SRP018856_adipose	0.00 RPM	76.77 RPM
SRP035408_brain	0.13 RPM	32.52 RPM
SRP035408_liver	0.09 RPM	57.45 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_11 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_11 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_11 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009888	2 retrocopies	retro_chof_2395, retro_chof_670,
Oryctolagus cuniculus	ENSOCUG00000003783	1 retrocopy	retro_ocun_904,
Rattus norvegicus	ENSRNOG00000020271	1 retrocopy	retro_rnor_2547,
Sus scrofa	ENSSSCG00000010685	1 retrocopy	retro_sscr_11 ,