RetrogeneDB ID: retro_ocun_1521

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:85856300..85858330(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: BMS1
• Ensembl ID: ENSOCUG00000005354
• Aliases: None
• Description: BMS1 ribosome biogenesis factor [Source:HGNC Symbol;Acc:23505]

Sequence

>retro_ocun_1521
ACTGGCCAATGCACTGCTGAGGAGGCGTTCGGCTCTGAGGATGAATCTGAAGAAGGCTCCTCGCTCAGTTCCGAGGAGGA
GGGCTCAGAAAATGAGGAGGTTCCTAGGGAAAAACCTTCAGAACCTTCCCAAGCGGGCAGGGGTCGGAAACCAGGCTCAG
AGAACTTAACTAGCGAGACCAGCGACATAGAGGAAATACTAAAGGAGGAGGAAGAGTACACAGAAGAAAATAGCTATTCC
ACAGAAACTTCAGGGGACCTCGAGTGGAAAGAAGACCTTTCTAGAAAGGCAGCGGAGGCCTTTTTGAGGCAGCAGCAAGC
GGCTGCAAATCTTCAGAAGCTTATTTATGGGACAGTGATGGAGGATAATGAAGAGGAAGAGGGCGATCCCCGAGAAGAGC
TCGGCGGGTTGTTCCGCGTCAGCTAGCCTGACAGAGGGTGCAAGCACAAGGCTGATTCCTTGGACGGCTCCAGGTTTCCC
GTGGAGGCACCCGACGACTGGGATTTAGAGGAGGTTATGAACAGCATCAGAGATCGCTTCGTGACTGGCAAGTGGGAGGA
AGACAAAGGTGCTGCCAAGATCTTAGCAGAAGATGAGGAGCTCTATGGTGACTTTGAAGACCTGGAAACAGGGGGTGTGC
ACGAAGGGAAATCAGGCCCAGATACTCAGACTGAAGATGTAGCAGAAGAAAAGGAAGAACTTGACCCCAGTGCAGAGGAA
ACTGCCCCCCCCCCCAAAAAAAGGCATTTGGATAAGAAGAGAAAATTGAAAGAGCTGTTTGATGCAGAAGATGATGAAGG
AGAAAGCACGTATTTCGATGATCTCAAAGGAGAAATGCAGAAACAAGCACAGCTTAACCGGGCAGAATTTGAAGACCAAG
ATGATGAAGCCAGAGTCCAGTATGAAGGTTTTCGACCTGGGATGTATGTTTGAATTGAGCTTGAAAATGTTCCCTGTGAA
TTTGTGCTCAACTTTGACCCTCATTACCCAGTTATTCTGGGTGGTTTGGGCAATGGTGAGGGCAACAGTGAATACGTGCA
GATGCGTCTCAAGAAACATCGTTGGTATAAGAAGATCTTCAAGTCCCGAGATCCAATCATTTTTTCTGTGGGGTGGAGCC
TATTTCAGACCATCCCACTTTATTATATTGAAGACCACAACGGAAGACAGAGACTTCTGAAGTACACCTCACAGCACATG
CACTGTGGAGCGACCTTCTCAGGTCCTATCACTCCACAGGGACCTGGCTTCTTGGCAGTGCAGTCTGTCAGTGGCATAAT
GCCTGATTTCTGAATCGCTGCAACAGGTGTCCTTGACCTGGGTACATCCATAAAGATTGTGAGGAAATTAAATCTAACTG
GATTTCATATAAAATTTTCAAGAATACTTCATTTATTAAGGGAATGTTTAATTCAGCTTTGGAAGTGGCCAAATTTGAAG
GTTTTGTGATTTGAACTGTCAGTGGGATCAGGGGACAGATAAAGAAGGCGCTCCAGGCTCCAGAGGGAGCTTTCCGGGTC
AGCTTTGAGGATAAGTTGCTGATGAGTGATATCCTCTTCATGCGAACTTGGTATCCTGTCTCCATTCCAGCCTTCTACAA
CCCCGTAACATCTTTGTTAAAACCACTGGGCGGGAAAGCTGCATGGTCAGGAATGCCGACCACAGGTCAACTCAGGCTTG
CGCAGGGCATCAAGCTGAAGCCGATCAAGGACTCCCTGTATAAGCCAATCCTGAGGCAAAGGAAGCATTTCAATTCACTG
CACATTCCAAAAGCCTTGCAGAAGGCCCTGCCATTTAAGAATAAGCCCAAGACTCAGGCAAAGGCAGTCAAGGTGCCAAA
GGACCGAGAGAGACCAGCCGTCATCCGGGAGCCTCATGAGAGGAAGATCCTGGCGCTGCTGGACACTCTGAGTGCGGTGC
ACAGTCAGAAGATGAGGAAGGCCAAGGAGCAGCGGCACCTGCACAACAAAGAGCACCTCCGAGTGAAGCAGCAGGAGGAA
GAGGAGAAGCTGAAGCGGCAGAAGGACCTG

Alignment

ORF - retro_ocun_1521 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.99 %
• Parental protein coverage: 52.73 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SGHCTAEEAFGSEDESEEGSSLSSQEEGSESEEVPRGKLAEPSQAGRRWTPGSENLASETSDIEDLLKEE
          .G.CTAEEAFGSEDESEEGSSLSS.EEGSE.EEVPR.K..EPSQAGR...PGSENL.SETSDIE..LKEE
Retrocopy TGQCTAEEAFGSEDESEEGSSLSSEEEGSENEEVPREKPSEPSQAGRGRKPGSENLTSETSDIEEILKEE

Parental  EEYTEEKSYSTETSGALKWKEDLSRKAAEAFLRQQQAAPNLRKLIYGTVTEDNEEEEGDPREELGGLFRV
          EEYTEE.SYSTETSG.L.WKEDLSRKAAEAFLRQQQAA.NL.KLIYGTV.EDNEEEEGDPREELGGLFRV
Retrocopy EEYTEENSYSTETSGDLEWKEDLSRKAAEAFLRQQQAAANLQKLIYGTVMEDNEEEEGDPREELGGLFRV

Parental  SQPDRGCKHKADSLDCSRFPVEAPHDWDLEEVMNSIRDCFVTGKWEEDKDAAKILAEDEELYGDFEDLET
          S.PDRGCKHKADSLD.SRFPVEAP.DWDLEEVMNSIRD.FVTGKWEEDK.AAKILAEDEELYGDFEDLET
Retrocopy S*PDRGCKHKADSLDGSRFPVEAPDDWDLEEVMNSIRDRFVTGKWEEDKGAAKILAEDEELYGDFEDLET

Parental  GDVHKGKSGPDTQIEDVAEEKEELDPSAEETA---KKKHLDKKRKLKELFDAEYDEGESTYFDDLKGEMQ
          G.VH.GKSGPDTQ.EDVAEEKEELDPSAEETA...KK.HLDKKRKLKELFDAE.DEGESTYFDDLKGEMQ
Retrocopy GGVHEGKSGPDTQTEDVAEEKEELDPSAEETAPPPKKRHLDKKRKLKELFDAEDDEGESTYFDDLKGEMQ

Parental  KQAQLNRAEFEDQDDEARVQYEGFRPGMYVRIELENVPCEFVLNFDPHYPVILGGLGNSEGNVGYVQMRL
          KQAQLNRAEFEDQDDEARVQYEGFRPGMYV.IELENVPCEFVLNFDPHYPVILGGLGN.EGN..YVQMRL
Retrocopy KQAQLNRAEFEDQDDEARVQYEGFRPGMYV*IELENVPCEFVLNFDPHYPVILGGLGNGEGNSEYVQMRL

Parental  KKHRWYKKILKSRDPIIFSVGWRRFQTIPLYYIEDHNGRQRLLKYTPQHMHCGATFWGPITPQGTGFLAV
          KKHRWYKKI.KSRDPIIFSVGW..FQTIPLYYIEDHNGRQRLLKYT.QHMHCGATF.GPITPQG.GFLAV
Retrocopy KKHRWYKKIFKSRDPIIFSVGWSLFQTIPLYYIEDHNGRQRLLKYTSQHMHCGATFSGPITPQGPGFLAV

Parental  QSVSGVMPDFRIAATGVVLDLDKSIKIVKKLKLTGF-PYKIFKNTSFIKGMFNSALEVAKFEGAVIRTVS
          QSVSG.MPDF.IAATG.VLDL..SIKIV.KL.LTGF..YKIFKNTSFIKGMFNSALEVAKFEG.VI.TVS
Retrocopy QSVSGIMPDF*IAATG-VLDLGTSIKIVRKLNLTGF<SYKIFKNTSFIKGMFNSALEVAKFEGFVI*TVS

Parental  GIRGQIKKALRAPEGAFRASFEDKLLMSDIVFMRTWYPVSIPAFYNPVTSLLKPLGEKDTWSGMRTTGQL
          GIRGQIKKAL.APEGAFR.SFEDKLLMSDI.FMRTWYPVSIPAFYNPVTSLLKPLG.K..WSGM.TTGQL
Retrocopy GIRGQIKKALQAPEGAFRVSFEDKLLMSDILFMRTWYPVSIPAFYNPVTSLLKPLGGKAAWSGMPTTGQL

Parental  RLAQGIKLKPNKDSLYKPILRQRKHFNSLHIPKALQKALPFKNKPKTQAKAGKVPKDRVRPAVIREPHER
          RLAQGIKLKP.KDSLYKPILRQRKHFNSLHIPKALQKALPFKNKPKTQAKA.KVPKDR.RPAVIREPHER
Retrocopy RLAQGIKLKPIKDSLYKPILRQRKHFNSLHIPKALQKALPFKNKPKTQAKAVKVPKDRERPAVIREPHER

Parental  KIRALLDALSTVHSQKMRKAKEQRHLHNKEHLRAKQKEEEEKLKRQKDL
          KI.ALLD.LS.VHSQKMRKAKEQRHLHNKEHLR.KQ.EEEEKLKRQKDL
Retrocopy KILALLDTLSAVHSQKMRKAKEQRHLHNKEHLRVKQQEEEEKLKRQKDL

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	0.00 RPM	38.58 RPM
SRP017611_kidney	0.00 RPM	39.63 RPM
SRP017611_liver	0.00 RPM	20.04 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1521 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1521 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1521 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000005354	1 retrocopy	retro_ocun_1521 ,