RetrogeneDB ID: retro_sscr_84

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:90213941..90214679(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000011673
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TSPAN6
• Ensembl ID: ENSSSCG00000012481
• Aliases: None
• Description: Sus scrofa tetraspanin 6 (TSPAN6), mRNA. [Source:RefSeq mRNA;Acc:NM_001244061]

Sequence

>retro_sscr_84
ATGGCGTCCCCGTCTCGGAGGCTGCAGACCAAACCGGTGATCACTTGTTTCAAGAGCGTCCTCTTGATCTACACATTCAT
CTTCTGGATCACCGGTGTAATCCTTCTTGCCGTTGGCATTTGGGGCAAGGTGAGCCTAGAGAATTATTTTTCCCTTTTAA
ATGAGAAGGCCACCAATGTCCCCTTCGTGCTCATTGGCACCGGCACTGTCATCATTCTATTGGGCACCTTCGGTTGTTTT
GCTACCTGCCGAGCTTCTGCATGGATGCTAAAACTGTATGCAATGTTTCTGACTCTTATTTTTTTGGTCGAACTGGTCGC
TGCCATCGTAGGATTTGTTTTCAGACATGAGATTAAGAACAGCTTTAAGAATAATTATGAGAAAGCGTTAAAACAATATA
ATGCTACGGGAGATTATAGAAGCGATGCAGTAGACAAGATCCAAAATACATTGCATTGTTGTGGTGTCACCGACTATAGA
GATTGGAAGGATACTAATTATTATTCAGAGAAAGGATTTCCCAAGAGCTGCTGTAAACTTGAAGGTTGTTCTCCTCAGAG
AGATGCAGATAAAGTAAACAATGAAGGTTGTTTTATAAAAGTGATGACCATTATAGAGTCAGAAATGGGCGTTGTTGCGG
GAATTTCCTTTGGAGTTGCTTGCTTCCAGCTGATCGGAATCTTTCTAGCCTACTGCCTCTCTCGTGCCATAACAAATAAC
CAGTATGAGATAGTGTAA

Alignment

ORF - retro_sscr_84 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASPSRRLQTKPVITCFKSVLLIYTFIFWITGVILLAVGIWGKVSLENYFSLLNEKATNVPFVLIGIGTV
          MASPSRRLQTKPVITCFKSVLLIYTFIFWITGVILLAVGIWGKVSLENYFSLLNEKATNVPFVLIG.GTV
Retrocopy MASPSRRLQTKPVITCFKSVLLIYTFIFWITGVILLAVGIWGKVSLENYFSLLNEKATNVPFVLIGTGTV

Parental  IILLGTFGCFATCRASAWMLKLYAMFLTLIFLVELVAAIVGFVFRHEIKNSFKNNYEKALKQYNATGDYR
          IILLGTFGCFATCRASAWMLKLYAMFLTLIFLVELVAAIVGFVFRHEIKNSFKNNYEKALKQYNATGDYR
Retrocopy IILLGTFGCFATCRASAWMLKLYAMFLTLIFLVELVAAIVGFVFRHEIKNSFKNNYEKALKQYNATGDYR

Parental  SDAVDKIQNTLHCCGVTDYRDWKDTNYYSEKGFPKSCCKLEGCSPQRDADKVNNEGCFIKVMTIIESEMG
          SDAVDKIQNTLHCCGVTDYRDWKDTNYYSEKGFPKSCCKLEGCSPQRDADKVNNEGCFIKVMTIIESEMG
Retrocopy SDAVDKIQNTLHCCGVTDYRDWKDTNYYSEKGFPKSCCKLEGCSPQRDADKVNNEGCFIKVMTIIESEMG

Parental  VVAGISFGVACFQLIGIFLAYCLSRAITNNQYEIV
          VVAGISFGVACFQLIGIFLAYCLSRAITNNQYEIV
Retrocopy VVAGISFGVACFQLIGIFLAYCLSRAITNNQYEIV

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	0.40 RPM	3.98 RPM
SRP014902_testis	4.10 RPM	36.92 RPM
SRP018288_heart	0.60 RPM	12.63 RPM
SRP018288_kidney	2.46 RPM	43.74 RPM
SRP018288_liver	5.44 RPM	89.55 RPM
SRP018288_lung	0.61 RPM	43.48 RPM
SRP018856_adipose	1.26 RPM	31.94 RPM
SRP035408_brain	1.65 RPM	59.33 RPM
SRP035408_liver	5.14 RPM	128.96 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

5 EST(s) were mapped to retro_sscr_84 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
EV949831	90213952	90214092	100	140	0	140
EW180485	90214319	90214421	100	102	0	102
EW397816	90214304	90214478	100	174	0	174
EW407999	90214213	90214328	100	115	0	115
EW656458	90214141	90214408	100	267	0	267

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_84 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_84 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017521	3 retrocopies	retro_cfam_1600, retro_cfam_1609, retro_cfam_878,
Callithrix jacchus	ENSCJAG00000004288	1 retrocopy	retro_cjac_2306,
Echinops telfairi	ENSETEG00000012276	1 retrocopy	retro_etel_1987,
Loxodonta africana	ENSLAFG00000027296	1 retrocopy	retro_lafr_994,
Microcebus murinus	ENSMICG00000011370	1 retrocopy	retro_mmur_447,
Nomascus leucogenys	ENSNLEG00000007505	1 retrocopy	retro_nleu_1186,
Otolemur garnettii	ENSOGAG00000004869	1 retrocopy	retro_ogar_2827,
Sarcophilus harrisii	ENSSHAG00000000274	1 retrocopy	retro_shar_515,
Sus scrofa	ENSSSCG00000012481	1 retrocopy	retro_sscr_84 ,