RetrogeneDB ID: retro_ocun_158

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018799:500868..502137(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021026
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000009154
• Aliases: None
• Description: None

Sequence

>retro_ocun_158
AGGAAACACCTCCAGGAGATTCCAGACCAGAGTGGCAACGTCACCACTAGTTTCACGTGGGGATGGGATTCCAGCAAGAC
TTCTGAACTGCTGTCAGGCATGGGGGTCTCCGCCCTGGAGAAGGAGGAAGTGGACAGTGAAAACATCCCCCAGGAACTGC
TCTCCAATGTGGGCCACCCACAGAGCCCCCCGCGGAAACGCCTGAAGAGCAAAGGCAATGAGAAAGACTTCGTGATCATC
CGCAGACCGAAGATCAATAGAGAAAATGTCCCAGGTGTTTCATGGGATTCCCTTCCCGATGAGCTGCTCCTGGGAATCTT
TTCCTGTCTCTGCCTCCCCGAGCTACTGAAAGTCTCCGGGGTTTGTAAGAGATGGTACTGCCTAGCGTTTGACGAGTCTC
TGTGGCAGACATTAGACCTCACAGGTAAAAATCTGCACCCTGATGTGATTGGCCGCTTGTTGTCTCGAGGGGTGGTTGCC
TTCCGCTGCCCGCGATCATTTATGGACCGACCATTGGTTGAACATTTCAGCTCTTTCCGTGTGCAGCACATGGACCTGTC
GAACTCAGTAATAAACGTGTCTACCCTTCACGGCATTCTGTCTCAGTGCTCCAAGTTGCAAAACCTAAGCCTGGAAGGCC
TACAGCTTTCGGATCTCATCGTCAATAATCTTGCACAGAACTCAAATTTAATGCGACTAAACCTTTGTGGGTGTTCTGGA
TTCTCTGAATCTGCCCTGAAGACTTTGCTAAGTGGCTGCTCCAGACTGGATGAGCTGAACCTCTCCTGGTGCTATGACTT
CACTGAGAAGCACGTGCAGGTGGCTGTGGCGCATGTCTCAGAGACCATCACCCAGCTGAATCTTAGTGGCTACCGAAAGA
ATCTCCAAAAGTCAGATGTCTCTACCCTAGTTAGAAGATGCCCCAATCTTGTCCACCTAGACTTAAGTGACAGCATCATG
CTAAAGAATGACTGCTTTCCGGAATTTCACCAGCTCAACTACCTCCAACACCTCTCACTCAGTCGATGCTATGATATAAT
ACCTGAAACTTTACTTGAACTTGGAGAAATTCCCACGCTAAAAACACTACAAGTTTTCGGAATCGTGCCAGACGGAACCC
TCCAACTGCTAAGGGAAGCCCTTCCTCATCTACAGATTAATTGCTCCCATTTTACCACCATTGCCAGGCCAACTATTGGC
AACAAAAAGAACCAGGAGATATGGGGCATCAAATGCCGACTGACACTGCAGAAACCCAGTTGTCTATGA

Alignment

ORF - retro_ocun_158 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 99.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RKHLQEIPDQSGNVTTSFTWGWDSSKTSELLSGMGVSALEKEEVDSENIPQELLSNVGHPQSPPRKRLKS
          RKHLQEIPDQSGNVTTSFTWGWDSSKTSELLSGMGVSALEKEEVDSENIPQELLSNVGHPQSPPRKRLKS
Retrocopy RKHLQEIPDQSGNVTTSFTWGWDSSKTSELLSGMGVSALEKEEVDSENIPQELLSNVGHPQSPPRKRLKS

Parental  KGNEKDFVIIRRPKINRENVPGVSWDSLPDELLLGIFSCLCLPELLKVSGVCKRWYCLAFDESLWQTLDL
          KGNEKDFVIIRRPKINRENVPGVSWDSLPDELLLGIFSCLCLPELLKVSGVCKRWYCLAFDESLWQTLDL
Retrocopy KGNEKDFVIIRRPKINRENVPGVSWDSLPDELLLGIFSCLCLPELLKVSGVCKRWYCLAFDESLWQTLDL

Parental  TGKNLHPDVIGRLLSRGVVAFRCPRSFMDRPLVEHFSSFRVQHMDLSNSVINVSTLHGILSQCSKLQNLS
          TGKNLHPDVIGRLLSRGVVAFRCPRSFMDRPLVEHFSSFRVQHMDLSNSVINVSTLHGILSQCSKLQNLS
Retrocopy TGKNLHPDVIGRLLSRGVVAFRCPRSFMDRPLVEHFSSFRVQHMDLSNSVINVSTLHGILSQCSKLQNLS

Parental  LEGLQLSDLIVNNLAQNSNLMRLNLCGCSGFSESALKTLLSGCSRLDELNLSWCYDFTEKHVQVAVAHVS
          LEGLQLSDLIVNNLAQNSNLMRLNLCGCSGFSESALKTLLSGCSRLDELNLSWCYDFTEKHVQVAVAHVS
Retrocopy LEGLQLSDLIVNNLAQNSNLMRLNLCGCSGFSESALKTLLSGCSRLDELNLSWCYDFTEKHVQVAVAHVS

Parental  ETITQLNLSGYRKNLQKSDVSTLVRRCPNLVHLDLSDSIMLKNDCFPEFHQLNYLQHLSLSRCYDIIPET
          ETITQLNLSGYRKNLQKSDVSTLVRRCPNLVHLDLSDSIMLKNDCFPEFHQLNYLQHLSLSRCYDIIPET
Retrocopy ETITQLNLSGYRKNLQKSDVSTLVRRCPNLVHLDLSDSIMLKNDCFPEFHQLNYLQHLSLSRCYDIIPET

Parental  LLELGEIPTLKTLQVFGIVPDGTLQLLREALPHLQINCSHFTTIARPTIGNKKNQEIWGIKCRLTLQKPS
          LLELGEIPTLKTLQVFGIVPDGTLQLLREALPHLQINCSHFTTIARPTIGNKKNQEIWGIKCRLTLQKPS
Retrocopy LLELGEIPTLKTLQVFGIVPDGTLQLLREALPHLQINCSHFTTIARPTIGNKKNQEIWGIKCRLTLQKPS

Parental  CL
          CL
Retrocopy CL

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	0.11 RPM	2.65 RPM
SRP017611_kidney	0.51 RPM	1.62 RPM
SRP017611_liver	0.00 RPM	3.16 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_158 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_158 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_158 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013562	4 retrocopies	retro_btau_1108, retro_btau_1612, retro_btau_525, retro_btau_555,
Choloepus hoffmanni	ENSCHOG00000006980	1 retrocopy	retro_chof_1604,
Callithrix jacchus	ENSCJAG00000018275	1 retrocopy	retro_cjac_2367,
Cavia porcellus	ENSCPOG00000013303	1 retrocopy	retro_cpor_1166,
Nomascus leucogenys	ENSNLEG00000016025	1 retrocopy	retro_nleu_2553,
Oryctolagus cuniculus	ENSOCUG00000009154	1 retrocopy	retro_ocun_158 ,
Pelodiscus sinensis	ENSPSIG00000008375	1 retrocopy	retro_psin_28,
Rattus norvegicus	ENSRNOG00000016823	1 retrocopy	retro_rnor_621,
Tupaia belangeri	ENSTBEG00000016814	1 retrocopy	retro_tbel_4354,