RetrogeneDB ID: retro_ocun_252

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:80316956..80317952(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023997
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SSBP3
• Ensembl ID: ENSOCUG00000005903
• Aliases: None
• Description: single stranded DNA binding protein 3 [Source:HGNC Symbol;Acc:15674]

Sequence

>retro_ocun_252
ATGTACGGCAAAGGCAAGAGTAACAGTAGCGCCGTCCCGTCCGACAGCCAGGCCCGGGAGAAGTTAGCACTCTATGTATA
TGAATATCTGCTCCATGTAGGAGCTCAGAAATCGGCCCAAACATTTTTATCAGAGATAAGACGGGAAAAAAACATCACAT
TGGGGGAACCACCAGGATTCTTGCATTCTTGGTGGTGTGTGTTCTGGGATCTCTACTATGCAGCCCCAGAGAGGCGGGAA
ACATGCGAGCATTCAAGCGAAGCGAAAGCCTTCCATGATTATCCATTCATGTCACCTCGGTACCCTGGAGGTCCAAGGCC
CCCATTGAGGATCCCTAATCAGGCACTTGGAGGTGTCCCAGGAAGTCAGCCATTACTCCCCAGTGGAATGGACCCAACCC
GACAACAAGGACATCCAAATATGGGTGGGCCAATGCAGAGAATGACTCCCCCACGAGGGATGGTGCCCTTAGGACCACAG
AGCTATGGAGGTGCCATGAGACCCCCACTGAATGCTTTAGGTGGCCCCGGAATGCCTGGAATGAACATGGGTCCAGGTGG
TGGCAGACCTTGGCCAAACCCAACAAATGCCAATTCAATACCATACTCCTCAGCATCTCCCGGGAATTATGTAGGTCCAC
CAGGAGGCGGAGGGCCACCAGGGACACCCATCATGCCCAGTCCAGCAGACTCAACCAACTCGGGAGACAACATGTATACT
TTAATGAATGCGGTACCTCCTGGACCCAACAGGCCTAATTTCCCGATGGGCCCCGGGTCAGATGGCCCCATGGGTGGATT
AGGAGGAATGGAGTCACATCACATGAATGGCTCATTAGGCTCAGGAGATATGGACAGTATTTCCAAGAACTCTCCCAATA
ACATGAGCCTGAGTAATCAGCCGGGCACCCCGAGGGATGATGGCGAGATGGGGGGAAGCTTCTTAAATCCTTTTCAGAGT
GAGAGCTACTCCCCGAGCATGACCATGAGCGTGTGA

Alignment

ORF - retro_ocun_252 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.08 %
• Parental protein coverage: 66.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPHAQPPPHNASSMMGAHSQPFMSPRYAGGPRPPIRMGNQPPGGVPGTQPLLPNSMDPTRQQGHPNMGGS
          .P.........S.....H..PFMSPRY.GGPRPP.R..NQ..GGVPG.QPLLP..MDPTRQQGHPNMGG.
Retrocopy APERRETCEHSSEAKAFHDYPFMSPRYPGGPRPPLRIPNQALGGVPGSQPLLPSGMDPTRQQGHPNMGGP

Parental  MQRMNPPRGMGPMGPGPQNYGSGMRPPPNSLG-PAMPGINMGPGAGRPWPNPNSANSIPYSSSSPGTYVG
          MQRM.PPRGM.P.GP..Q.YG..MRPP.N.LG.P.MPG.NMGPG.GRPWPNP..ANSIPYSS.SPG.YVG
Retrocopy MQRMTPPRGMVPLGP--QSYGGAMRPPLNALGGPGMPGMNMGPGGGRPWPNPTNANSIPYSSASPGNYVG

Parental  PPGGGGPPGTPIMPSPADSTNSSDNIYTMINPVPPGGSRANFPMGPGSDGPMGGMGGMEPHHMNGSLGSG
          PPGGGGPPGTPIMPSPADSTNS.DN.YT..N.VPPG..R.NFPMGPGSDGPMGG.GGME.HHMNGSLGSG
Retrocopy PPGGGGPPGTPIMPSPADSTNSGDNMYTLMNAVPPGPNRPNFPMGPGSDGPMGGLGGMESHHMNGSLGSG

Parental  DIDGLPKNSPNNISGISNPPGTPRDDGELGGNFLHSFQNDNYSPSMTMSV
          D.D...KNSPNN.S..SN.PGTPRDDGE.GG.FL..FQ...YSPSMTMSV
Retrocopy DMDSISKNSPNNMS-LSNQPGTPRDDGEMGGSFLNPFQSESYSPSMTMSV

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	6.29 RPM	116.06 RPM
SRP017611_kidney	2.94 RPM	54.53 RPM
SRP017611_liver	0.77 RPM	11.56 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_252 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_252 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_252 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005029	1 retrocopy	retro_cjac_3827,
Homo sapiens	ENSG00000157216	6 retrocopies	retro_hsap_1302, retro_hsap_1384, retro_hsap_2155, retro_hsap_2319, retro_hsap_2539, retro_hsap_3721,
Macropus eugenii	ENSMEUG00000009291	1 retrocopy	retro_meug_1372,
Oryctolagus cuniculus	ENSOCUG00000005903	1 retrocopy	retro_ocun_252 ,
Pan troglodytes	ENSPTRG00000000770	2 retrocopies	retro_ptro_2618, retro_ptro_2931,