RetrogeneDB ID: retro_ocun_1239

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:73185239..73186514(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000026122
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SF3B4
• Ensembl ID: ENSOCUG00000004614
• Aliases: None
• Description: splicing factor 3b, subunit 4, 49kDa [Source:HGNC Symbol;Acc:10771]

Sequence

>retro_ocun_1239
ATGGCTGCCGGGCCGATCTCCGAGCGGAACCAGGATGCTACTGTGTACGTGGGGGGCCTGGACGAGAAGGTTAGCAAACC
TCTGCTGTGGGAGCTCTTCCTGCAGGCAGGACCGGTGGTCAACACTCACATGCCGAAGGACAGAGTCACTGGCCAGCACC
AAGGCTATGGCTTTGTGGAATTCTTGAGTGAAGAAGATGCTGACTATGCCATTAAGATCATGAACATGATCAAACTCTAT
GGGAAGCCAATACGAGTGAACAAGGCATCAGCTCACAACAAAAACCTGGATGTGGGGGCCAACATTTTCATCGGGAACCT
GGACCCGGAGATTGACGAGAAGCTGCTTTACGATACTTTTAGCGCCTTTGGGGTCATCTTACAACCCCCAAGATCATGCG
GGACCCTGACACAGGCAACTCCAAAGGTTATGCCTTTATTAATTTCGCTTCATTTGATGCCTCGGATGCAGCAATTGAGG
CCATGAATGGGCAGTACCTCTGTAACCGCCCCATCACCGTGTCTTATGCCTTCAAGAAGGACTCCAAGGGTGAGCGCCAT
GGCTCCGCAGCTGAACGACTTCTGGCAGCCCAGAACCCACTCTCCCAGGCTGATCGCCCGCATCAGCTGTTTGCAGATGC
ACCCCCTCCACCCTCTGCTCCCAACCCTGTGGTATCATCACTGGGGTCTGGGCTTCCTCCACCAGGCATGCCTCCTCCTG
GCTCTTTCCCACCCCCAGTGCCGCCTCCTGGAGCCCTCCCACCTGGAATACCTCCAGCCATGCCCCCCCCACCAATGCCT
CCTGGGGCTGGAGGACATGGCCCTCCATCAGCAGGCACCCCGGGGGCTGGACATCCTGGTCATGGACACTCACATCCTCA
CCCCTTCCCACCAGGTGGCATGCCCCATCCAGGGATGTCTCAGATGCAGCTGGCCCACCATGGCCCTCATGGCTTAGGAC
ACCCCCATGCTGGGCCCCCAGGCTCTGGGGGACAGCCACCACCACGCCCACCTCCTGGAATGCCTGCCTCATCCTGGACC
TCCTCCAATGGGCATGCCCCCCAGAGGACCTCCGTTTGGATCTCCCATGGGTCACCCAGGCCCTATGCCTCCACATGGTA
TGCGAGGACCCCCTCCACTGATGCCGCCTCATGGGTACACTGGTCCTCCACGGCCCCCGCCCTATGGCTACCAGCGGGGC
CCCCTTCCTCCACCCAGACCCACTCCCCGGCCTCCAGTTCCCCCTCGAGGCCCACTTCGGGGCCCTCTTCCTCAA

Alignment

ORF - retro_ocun_1239 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA
          MAAGPISERNQDATVYVGGLDEKVS.PLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA
Retrocopy MAAGPISERNQDATVYVGGLDEKVSKPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA

Parental  IKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQ-TPKIMRDPDTG
          IKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQ.TPKIMRDPDTG
Retrocopy IKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQ<TPKIMRDPDTG

Parental  NSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQ
          NSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQ
Retrocopy NSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQ

Parental  LFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPPPMPPGAGGHGPPSAG
          LFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPPPMPPGAGGHGPPSAG
Retrocopy LFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPPPMPPGAGGHGPPSAG

Parental  TPGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPG-PPP
          TPGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMP.....PP
Retrocopy TPGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPASS>GPP

Parental  -MGMPPRGPPFGSPMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGP
          .MGMPPRGPPFGSPMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGP
Retrocopy PMGMPPRGPPFGSPMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGP

Parental  LRGPLPQ
          LRGPLPQ
Retrocopy LRGPLPQ

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	0.61 RPM	24.78 RPM
SRP017611_kidney	2.53 RPM	18.14 RPM
SRP017611_liver	0.15 RPM	7.40 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1239 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1239 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1239 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012495	2 retrocopies	retro_btau_1385, retro_btau_592,
Canis familiaris	ENSCAFG00000011617	3 retrocopies	retro_cfam_585, retro_cfam_711, retro_cfam_729,
Callithrix jacchus	ENSCJAG00000000793	3 retrocopies	retro_cjac_1297, retro_cjac_1909, retro_cjac_638,
Cavia porcellus	ENSCPOG00000008267	1 retrocopy	retro_cpor_234,
Echinops telfairi	ENSETEG00000008963	1 retrocopy	retro_etel_1310,
Homo sapiens	ENSG00000143368	1 retrocopy	retro_hsap_1356,
Gorilla gorilla	ENSGGOG00000004761	1 retrocopy	retro_ggor_1056,
Macaca mulatta	ENSMMUG00000007256	1 retrocopy	retro_mmul_2191,
Mustela putorius furo	ENSMPUG00000005563	2 retrocopies	retro_mputfur_1105, retro_mputfur_648,
Oryctolagus cuniculus	ENSOCUG00000003342	1 retrocopy	retro_ocun_924,
Oryctolagus cuniculus	ENSOCUG00000004614	1 retrocopy	retro_ocun_1239 ,
Pongo abelii	ENSPPYG00000000912	1 retrocopy	retro_pabe_1124,
Pan troglodytes	ENSPTRG00000001243	1 retrocopy	retro_ptro_930,
Pteropus vampyrus	ENSPVAG00000014171	1 retrocopy	retro_pvam_931,
Rattus norvegicus	ENSRNOG00000021181	1 retrocopy	retro_rnor_2350,
Ictidomys tridecemlineatus	ENSSTOG00000000684	2 retrocopies	retro_itri_1153, retro_itri_487,