RetrogeneDB ID: retro_ocun_1222

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:13736904..13738989(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000024138
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TTC7B
• Ensembl ID: ENSOCUG00000008905
• Aliases: None
• Description: tetratricopeptide repeat domain 7B [Source:HGNC Symbol;Acc:19858]

Sequence

>retro_ocun_1222
GGACTGTGTTTAGAGAAGCTGCCTATCTCGTCTTCTACCAGTAACCTCCACGTGGACCGGGAGCAGGATGTCATCACCTG
TTACGAGAAAGCGGGGGACATCGCCCTCCTGTACCTCCAGGAGATAGAGAGGGTAATACTTTCTAATATTCAGAACAGAA
GCCCCAAGCCTGGCCCTGCTCCCCACGATCAAGAACTAGGGTTTTTCCTAGAAACAGGACTTCAGAGAGCCCATGTCCTC
TATTTCAAAAATGGGAACTTGACGAGAGGAGTCGGGAGATTCAGAGAGATCCTCAGAGCAGTCGAAACAAGGACCACTCA
AAACCTGCGAATGACGATAGCCAGGCAGCTGGCCGAGATCCTGCTGCGGGGCATGTGTGAGCAGAGCTACTGGAACCCCC
TGGAGAGCCCGCCCTGCCAGTTGCCTCTGGACGACCCTCTCCGGAAAGGAGCCAACACGAAAACCTACACCCTCACCCGC
AGAGCCCGCGTCTACGCAGGAGAGAACATTTTTTGTCCTCAAGAAAACACTGAAGAAGCCCTGTTGTTACTGCTGATTAG
TGAATCAATGGCCAACCGGGACGCTGTGCTAAGCAGGATCCCCGAGCACAAGAGTGACTGCCTCATCAGCCTGCAGAGTG
CGTCTGTGGTCTATGACTTACTGACCATTGCTCTGGGAAGAAGAGGCCAGTATGAGATGCTGTCGGAGTGCTTAGAAAGA
GCCATGAAGTTTGCCTTCGAGGAGTTCCACCTCTGGTACCAGTTTGCTCTCTCGCTAATGGCTGCTGGGAAATCCGCCCG
AGCCGTGAAGGTGCTGAAGGAGTGCATCCGCCTGAAGCCCGACGACGCCACCATCCCTCTGCTCGCCGCCAAGCTGTGCA
TGGGCTCCCTGCACTGGCTGGAAGAAGCTGAAAATTTTGCCAAAACTGTTGTCGATGTGGGAGAGAAAACATCCGAGTTC
AAGGCCAAAGGCTACTTAGCTCTGGGACTCACGTACAGCCTGCAGGCCACTGATGCTTCTTTGCGAGGGATGCAGGAGGT
CCTGCAGAGAAAGGCGCTGCTCGCGTTTCAGAGGGCCCACAGCCTGTCGCCTACAGATCACCAGGCTGCCTTCTACCTGG
CTCTGCAGCTTGCCATCTCCAGGCAGATACCGGAGGCTTTGGGGTACGTCCGCCAAGCTCTTCAACTTCAGGGGGATGAT
GCCAACTCCCTGCACCTGCTCGCCCTCCTCCTGTCAGCACAAAAACACTACCACGACGCTCTGAACATCATCGACATGGC
CCTGAGCGAATATCCAGAAAATTTCATACTGCTGTTCTCCAAAGTGAAGTTGGAGTCGCTCTGCCGGGGCCCGGATGAGG
CGCTCCTCACCTGTAAGCACATGTTACAAATATGGAAATCCTGCTACAACCTCACCAACCCCAGTGATTCGGGACGAGGG
AGCAGCCTCTTGGATCGGACCATCGCAGACAGACGGCAGCTGAACACCATCACTTTGCCAGACTTCAGCGATCCCGAGAC
AGGCTCTGTCCACGCCACGTCAGTAGCAGCCTCCAGGGTGGAGCAGGCTCTGTCGGAAGTGGCCTCGTCTCTGCAGAGCA
GCGCCCCCAAGCAGGGCCCACTACACCCCTGGATGACACTGGCACAGATCTGGCTCCACGCAGCGGAAGTCTACATCGGC
ATCGAGAAGCCCGCGGAAGCCACCGCCTGCACCCAGGAAGCTGCCAACCTCTTCCCAATGTCCCACAACGTGCTGTACAT
GCGGGGCCAGGTCGCTGAGCTCCGCGGCCACCTGGAGGAAGCCCAGCGCTGGTATGAGGAAGCCTTGTCCATCAGCCCCA
CCCACGTGAAGAGCATGCAGCGACTGGCCCTGATCCTGCACCAGCTGGGCCGCTACAGCCTGGCGGAGAAGATCCTCCGG
GACGCGGTGCAGGTGAACTCCACGGCCCACGAGGTCTGGAACGGGCTGGGCGAGGTCCTCCAAGCGCAGGGCAACGACGC
GGCCGCCACCGAGTGCTTCCTGACCGCCCTGGAGCTGGAGGCCAGCAGCCCCGCCGTGCCCTTCACCATCATCCCCCGCG
TGCTG

Alignment

ORF - retro_ocun_1222 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLCLEKLPISSSTSNLHVDREQDVITCYEKAGDIALLYLQEIERVILSNIQNRSPKPGPAPHDQELGFFL
          GLCLEKLPISSSTSNLHVDREQDVITCYEKAGDIALLYLQEIERVILSNIQNRSPKPGPAPHDQELGFFL
Retrocopy GLCLEKLPISSSTSNLHVDREQDVITCYEKAGDIALLYLQEIERVILSNIQNRSPKPGPAPHDQELGFFL

Parental  ETGLQRAHVLYFKNGNLTRGVGRFREILRAVETRTTQNLRMTIARQLAEILLRGMCEQSYWNPLESPPCQ
          ETGLQRAHVLYFKNGNLTRGVGRFREILRAVETRTTQNLRMTIARQLAEILLRGMCEQSYWNPLESPPCQ
Retrocopy ETGLQRAHVLYFKNGNLTRGVGRFREILRAVETRTTQNLRMTIARQLAEILLRGMCEQSYWNPLESPPCQ

Parental  SPLDDPLRKGANTKTYTLTRRARVYAGENIFCPQENTEEALLLLLISESMANRDAVLSRIPEHKSDRLIS
          .PLDDPLRKGANTKTYTLTRRARVYAGENIFCPQENTEEALLLLLISESMANRDAVLSRIPEHKSD.LIS
Retrocopy LPLDDPLRKGANTKTYTLTRRARVYAGENIFCPQENTEEALLLLLISESMANRDAVLSRIPEHKSDCLIS

Parental  LQSASVVYDLLTIALGRRGQYEMLSECLERAMKFAFEEFHLWYQFALSLMAAGKSARAVKVLKECIRLKP
          LQSASVVYDLLTIALGRRGQYEMLSECLERAMKFAFEEFHLWYQFALSLMAAGKSARAVKVLKECIRLKP
Retrocopy LQSASVVYDLLTIALGRRGQYEMLSECLERAMKFAFEEFHLWYQFALSLMAAGKSARAVKVLKECIRLKP

Parental  DDATIPLLAAKLCMGSLHWLEEAENFAKTVVDVGEKTSEFKAKGYLALGLTYSLQATDASLRGMQEVLQR
          DDATIPLLAAKLCMGSLHWLEEAENFAKTVVDVGEKTSEFKAKGYLALGLTYSLQATDASLRGMQEVLQR
Retrocopy DDATIPLLAAKLCMGSLHWLEEAENFAKTVVDVGEKTSEFKAKGYLALGLTYSLQATDASLRGMQEVLQR

Parental  KALLAFQRAHSLSPTDHQAAFYLALQLAISRQIPEALGYVRQALQLQGDDANSLHLLALLLSAQKHYHDA
          KALLAFQRAHSLSPTDHQAAFYLALQLAISRQIPEALGYVRQALQLQGDDANSLHLLALLLSAQKHYHDA
Retrocopy KALLAFQRAHSLSPTDHQAAFYLALQLAISRQIPEALGYVRQALQLQGDDANSLHLLALLLSAQKHYHDA

Parental  LNIIDMALSEYPENFILLFSKVKLESLCRGPDEALLTCKHMLQIWKSCYNLTNPSDSGRGSSLLDRTIAD
          LNIIDMALSEYPENFILLFSKVKLESLCRGPDEALLTCKHMLQIWKSCYNLTNPSDSGRGSSLLDRTIAD
Retrocopy LNIIDMALSEYPENFILLFSKVKLESLCRGPDEALLTCKHMLQIWKSCYNLTNPSDSGRGSSLLDRTIAD

Parental  RRQLNTITLPDFSDPETGSVHATSVAASRVEQALSEVASSLQSSAPKQGPLHPWMTLAQIWLHAAEVYIG
          RRQLNTITLPDFSDPETGSVHATSVAASRVEQALSEVASSLQSSAPKQGPLHPWMTLAQIWLHAAEVYIG
Retrocopy RRQLNTITLPDFSDPETGSVHATSVAASRVEQALSEVASSLQSSAPKQGPLHPWMTLAQIWLHAAEVYIG

Parental  IGKPAEATACTQEAANLFPMSHNVLYMRGQVAELRGHLEEAQRWYEEALSISPTHVKSMQRLALILHQLG
          I.KPAEATACTQEAANLFPMSHNVLYMRGQVAELRGHLEEAQRWYEEALSISPTHVKSMQRLALILHQLG
Retrocopy IEKPAEATACTQEAANLFPMSHNVLYMRGQVAELRGHLEEAQRWYEEALSISPTHVKSMQRLALILHQLG

Parental  RYSLAEKILRDAVQVNSTAHEVWNGLGEVLQAQGNDAAATECFLTALELEASSPAVPFTIIPRVL
          RYSLAEKILRDAVQVNSTAHEVWNGLGEVLQAQGNDAAATECFLTALELEASSPAVPFTIIPRVL
Retrocopy RYSLAEKILRDAVQVNSTAHEVWNGLGEVLQAQGNDAAATECFLTALELEASSPAVPFTIIPRVL

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	21.69 RPM	38.08 RPM
SRP017611_kidney	6.59 RPM	13.89 RPM
SRP017611_liver	0.23 RPM	0.54 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1222 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1222 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1222 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
Myotis lucifugus	ENSMLUG00000005584	1 retrocopy	retro_mluc_616,
Oryctolagus cuniculus	ENSOCUG00000008905	1 retrocopy	retro_ocun_1222 ,