RetrogeneDB ID: retro_sscr_44

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:133606547..133607528(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000002608
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000025366
• Aliases: None
• Description: None

Sequence

>retro_sscr_44
ACGTGTCTCTTGACCTTGCAGGTGATCGACCCCATGAACGTCTCTGAGCCAGATTCCAGCTTTGCTTTTGTAAGAGAATT
TATACTCCTAGGTTTTTCTTGTGAGTGGAAGATTCAGATCCTCCTCTTCTCACTTCTCCTTACAACATATGCTCTGACCA
TAACAGGCAATGGGGCCATTGTTTGTGCGTTATGCTGTGACCGGCGACTCCACATCCCCATGTATATGTTCCTGGGGAAT
TTCTCCTTTCTAGAAATCTGGTATGTCTCGTCTACAACACCCAAGATGTTAATCAACTTCCTCTCAGACAAAAAGACCAT
CTCCTTTGTTGGATGTTTCCTCCAATTTTATTTCTTTTTTTCTTTGGGAACAAGTGAAAGCTTACTTTTGGCTGTCATGG
CCTTTGATCGGTACCTCGCTATCTGCCGTCCCTTGCACTACCCTAATCTCATGACTGGGCATCTCTGTACCAAACTGGTC
ATGACCTGCTGGGCTTGTGGGTTTCTGTGGTTCCTGATCCCCATTGTTCTCATCTCTCAGATGTCCTTCTGTGGATCAAA
CATTATTGACCATGTTGTGTGTGACCCAGGACCACTATTTGCACTGGCGTGTGTCTCTGCCCCAGCAACTCAACTGCTTT
GTTACACTCTAAGCTCTTTAGTTATCATTGGTAACTTTCTCTTCATCCTTGGGTCCTATACCCTTGTCCTAACAGCTGTG
TTACGGATGCCTTCAGCCACTGGGAGACATAAGGCCTTCTCCACTTGCGGGTCTCATTTGGCTGTGGTATCACTGTTCTA
TGGATCTCTGATGGTCATATATGTGAGCCCAGGACTCGGACATTCTGCTGCAATGCAGAAAGTTGCAACTTTGTTCTATG
CTATGGTGACCCCACTCTTCAATCCCTTCATCTATAGTTTCCGGAATAAGGAGATAAAGGCGGCCCTGAGGAAAGTTCTG
GGGAGCTTCAGTATATTCTAA

Alignment

ORF - retro_sscr_44 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.32 %
• Parental protein coverage: 95.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TLQYLKMGLGLENSIHFAFVREFILLGFSCEWKIQILLFSLFLTTYALTITGNGAIVCALCCDRRLHIPM
          TLQ........E....FAFVREFILLGFSCEWKIQILLFSL.LTTYALTITGNGAIVCALCCDRRLHIPM
Retrocopy TLQVIDPMNVSEPDSSFAFVREFILLGFSCEWKIQILLFSLLLTTYALTITGNGAIVCALCCDRRLHIPM

Parental  YMFLGNFSFLEIWYVSSTTPKMLINFLSDKKTISFVGCFLQFYFFFSLGTTECLLLAVMAFDRYLAICRP
          YMFLGNFSFLEIWYVSSTTPKMLINFLSDKKTISFVGCFLQFYFFFSLGT.E.LLLAVMAFDRYLAICRP
Retrocopy YMFLGNFSFLEIWYVSSTTPKMLINFLSDKKTISFVGCFLQFYFFFSLGTSESLLLAVMAFDRYLAICRP

Parental  LHYPNLMTGHLCTKLVMTCWACGFLWFL-PIVLISQMSFCGSNIIDHVVCDPGPLFALACVSAPATQLLC
          LHYPNLMTGHLCTKLVMTCWACGFLWFL.PIVLISQMSFCGSNIIDHVVCDPGPLFALACVSAPATQLLC
Retrocopy LHYPNLMTGHLCTKLVMTCWACGFLWFLIPIVLISQMSFCGSNIIDHVVCDPGPLFALACVSAPATQLLC

Parental  YTLSSLVIFGNFLFILGSYTLVLTAVLRMPSATGRHKAFSTCGSHLAVVSLFYGSLMVMYVSPGLGHSAA
          YTLSSLVI.GNFLFILGSYTLVLTAVLRMPSATGRHKAFSTCGSHLAVVSLFYGSLMV.YVSPGLGHSAA
Retrocopy YTLSSLVIIGNFLFILGSYTLVLTAVLRMPSATGRHKAFSTCGSHLAVVSLFYGSLMVIYVSPGLGHSAA

Parental  MQKVATLFYAMVTPLFNPFIYSFRNKEIKAALRKVLG
          MQKVATLFYAMVTPLFNPFIYSFRNKEIKAALRKVLG
Retrocopy MQKVATLFYAMVTPLFNPFIYSFRNKEIKAALRKVLG

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	0.00 RPM
SRP014902_testis	0.00 RPM	0.00 RPM
SRP018288_heart	0.00 RPM	0.00 RPM
SRP018288_kidney	0.00 RPM	0.00 RPM
SRP018288_liver	0.00 RPM	0.00 RPM
SRP018288_lung	0.00 RPM	0.00 RPM
SRP018856_adipose	0.00 RPM	0.00 RPM
SRP035408_brain	0.03 RPM	0.00 RPM
SRP035408_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_44 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_44 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_44 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sus scrofa	ENSSSCG00000025366	1 retrocopy	retro_sscr_44 ,