RetrogeneDB ID: retro_ocun_148

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:64943271..64945170(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021198
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000010617
• Aliases: None
• Description: None

Sequence

>retro_ocun_148
ATGTCTTTGATTCCAGCAACACATTATATATATACACCCCTGAATCAGCTTAAAGGTGGTACAATTGTCAATGTCTATGG
TGTCGTGAAGTTCTTTAAGCCTCCATATCTAAGCAAAGGAACTGATTATTGTTCTGTTGTTACGATTGTGGACCAAACAA
ATGTAAAGTTGACCTGCCTGCTCTTTAGTGGAAACTATGAAGCCCTTCCAAAAATTTATAAAATTGGAGATATTGTTCGC
TTTCATAGACTGAAGATTCAAGAATATAAAAAGGAAACTCAAGGTATCACCAGCTCTGGCTTTGCATCGTTGACCTTTGA
GGTAACTCTGGGCGCCCCTGTCATACCTCGTACTTCAAGCAAGTATTTCAACTTCAGTACTAAGGACCACAAAATGGTAG
AAGCCTTACGTGTTTGGGCATCTTCTCATCTTTCACCTTCCTCAGCCTTATTAAAATTATGTGATGTTCAACCAATGCAG
TATTTTGACCTGACTTGTCAGCTTTTGGGCAAGGCAGAAGTTGATGGAGCATCATTTCTTCTAAAGGTGTGGGATGGCAA
TAGGACACCCTTCCCATCTTGGAGAGTCCTGATACAAGATCTTGTTCTCGAAGGTGATATAAGTCACATCCATCGGCTAC
AGAATCTGACAATAGACATTTTAGTCTATGATAACCATGTTCAAGTGGCAAGATCTTTAAAGATTGGAAGCTTTCTTAGA
ATCTATAGTCTCCATACCAAACTACAGTCAGTGCATTCAGAGAGCCAGGCAACATTGCTGTGTCTAGAGTTTCATCTCCA
TGGAGGTACCAGTTATGGCCGGGGAATCACGGTCTTGCCAGAAAGTAACTCTGATGTGGATCAGCTGAAAAAGGCTCTAG
AATCTGCAGATTTGACCAGTCAACATTCAGATCGTTTCTGTCAGTCAGAACATGAGGACAGTTTTCCAACTCCTTCAAGT
TCTGGATCAGTATCACTGTATGAGGTAGAAAGATGTCAACAGCTGTCTGCTACAATACTTACAGATCATCAGTATTTGGA
GAAAACACCACTGTGTGCAATTTTGAAACAAAAAACTCCTAAACAATATCGCATCCGAGCAAAATTGAGATCTTATAAGC
CCAAAAGTCTCTATCAGTCTGTTAAACTTCATTGTCCTAAATGTCATTCACTGCAGGAAGTTCCACAGGAAGGCAATTTG
GATATAATTTTGAAAGAAAATGCAACTAAAACCCCAGATACCAAACTACATAATACATTATTATATGATTTAAAAATTTG
GACCACAGAAGAACAAGGAGGACGAAAAGTAGCTGTTCATTTTGTGAAACATAATGGTATTCTTCCACTTTCAAATGAGT
GTCTAATTTTGATAGAAGGAGGTACACTCTCTGAAATCTATAAACTCGCAAATAAGTTTCATAGTGTAATTCCGGTGAAA
TCTGGCCAGGAAGATCTAGAACTCCTAGACCTTTCAGCACCATTCCTGATACAAGGAAAGATACTTCACTATGGATGTAA
ACAGTGTTCTAGTTTGAGATCAATACAAAATCTAAATTCTCTGGTTGATAAAATATCCTGGATTCCTTCTTCTGTGGCAG
AAGTATTGGGTATTGTGCCCCTCCAATATGTGTTTGTCATGACATTTACTCTTGATGATGGAACAGGAGTGTTGGAAGCT
TATCTTATGGATACTATTCCAGCATCAGAAATTCTAGCTGATGATGACTTCCAGAGAAGTATGGAAATGATCATGGATAT
GTTTTGTCCTCCAGGAAGAAAAATTGATGCATATCCATGGTTGGAATGCTTCCTCAAGTCATATAATGTCACAAATGGGA
CGGAGCAGCAAGTTTGCTATCAGATTTTTGACACCACAGTTGGAGAAGATGTTATCTAA

Alignment

ORF - retro_ocun_148 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.09 %
• Parental protein coverage: 90.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ISLIPATHYIYTPLNQLKGGTIVNVYGVVKFFKPPYLSKGTDYCSVVTIVDQTNVKLTCLLFSGNYEALP
          .SLIPATHYIYTPLNQLKGGTIVNVYGVVKFFKPPYLSKGTDYCSVVTIVDQTNVKLTCLLFSGNYEALP
Retrocopy MSLIPATHYIYTPLNQLKGGTIVNVYGVVKFFKPPYLSKGTDYCSVVTIVDQTNVKLTCLLFSGNYEALP

Parental  KIYKIGDIVRFHRLKIQEYKKETQGITSSGFASLTFEGTLGAPVIPRTSSKYFNFSTKDHKMVEALRVWA
          KIYKIGDIVRFHRLKIQEYKKETQGITSSGFASLTFE.TLGAPVIPRTSSKYFNFSTKDHKMVEALRVWA
Retrocopy KIYKIGDIVRFHRLKIQEYKKETQGITSSGFASLTFEVTLGAPVIPRTSSKYFNFSTKDHKMVEALRVWA

Parental  SSHLSPSSALLKLCDVQPMQYFDLTCQLLGKAEVDGASFLLKVWDGNRTPFPSWRVLIQDLVLEGDISHI
          SSHLSPSSALLKLCDVQPMQYFDLTCQLLGKAEVDGASFLLKVWDGNRTPFPSWRVLIQDLVLEGDISHI
Retrocopy SSHLSPSSALLKLCDVQPMQYFDLTCQLLGKAEVDGASFLLKVWDGNRTPFPSWRVLIQDLVLEGDISHI

Parental  HRLQNLTIDILVYDNHVQVARSLKIGSFLRIYSLHTKLQSVHSESQATLLCLEFHLHGGTSYGRGITVLP
          HRLQNLTIDILVYDNHVQVARSLKIGSFLRIYSLHTKLQSVHSESQATLLCLEFHLHGGTSYGRGITVLP
Retrocopy HRLQNLTIDILVYDNHVQVARSLKIGSFLRIYSLHTKLQSVHSESQATLLCLEFHLHGGTSYGRGITVLP

Parental  ESNSDVDQLKKALESADLTSQHSDRFCQSEHEDSFPTPSSSGSVSLYEVERCQQLSATILTDHQYLEKTP
          ESNSDVDQLKKALESADLTSQHSDRFCQSEHEDSFPTPSSSGSVSLYEVERCQQLSATILTDHQYLEKTP
Retrocopy ESNSDVDQLKKALESADLTSQHSDRFCQSEHEDSFPTPSSSGSVSLYEVERCQQLSATILTDHQYLEKTP

Parental  LCAILKQKTPKQYRIRAKLRSYKPKSLYQSVKLHCPKCHSLQEVPQEGNLDIILKENATKTPDTKLHNTL
          LCAILKQKTPKQYRIRAKLRSYKPKSLYQSVKLHCPKCHSLQEVPQEGNLDIILKENATKTPDTKLHNTL
Retrocopy LCAILKQKTPKQYRIRAKLRSYKPKSLYQSVKLHCPKCHSLQEVPQEGNLDIILKENATKTPDTKLHNTL

Parental  LYDSKIWTTEEQGGRKVAVHFVKHNGILPLSNECLILIEGGTLSEIYKLANKFHSVIPVKSGQEDLELLD
          LYD.KIWTTEEQGGRKVAVHFVKHNGILPLSNECLILIEGGTLSEIYKLANKFHSVIPVKSGQEDLELLD
Retrocopy LYDLKIWTTEEQGGRKVAVHFVKHNGILPLSNECLILIEGGTLSEIYKLANKFHSVIPVKSGQEDLELLD

Parental  LSAPFLIQGKILHYGCKQCSSLRSIQNLNSLVDKISWIPSSVAEVLGIVPLQYVFVMTFTLDDGTGVLEA
          LSAPFLIQGKILHYGCKQCSSLRSIQNLNSLVDKISWIPSSVAEVLGIVPLQYVFVMTFTLDDGTGVLEA
Retrocopy LSAPFLIQGKILHYGCKQCSSLRSIQNLNSLVDKISWIPSSVAEVLGIVPLQYVFVMTFTLDDGTGVLEA

Parental  YLMDTDKFFQIPASE
          YLMDT.....I.A..
Retrocopy YLMDTIPASEILADD

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
SRP017611_brain	1.43 RPM	3.81 RPM
SRP017611_kidney	1.72 RPM	6.08 RPM
SRP017611_liver	1.08 RPM	1.46 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_148 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_148 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_148 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010344	1 retrocopy	retro_dnov_1971,
Oryctolagus cuniculus	ENSOCUG00000010617	1 retrocopy	retro_ocun_148 ,