RetrogeneDB ID: retro_ocun_843

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:80358155..80358935(-)
• Located in intron of: ENSOCUG00000017220

Retrocopy information

• Ensembl ID: ENSOCUG00000026700
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BCCIP
• Ensembl ID: ENSOCUG00000008761
• Aliases: None
• Description: BRCA2 and CDKN1A interacting protein [Source:HGNC Symbol;Acc:978]

Sequence

>retro_ocun_843
GAGGAAGTGAATATTGATTTTGAAGCTTACTCCATCTCAGATAATGATTATGACGGAATTAAGAAATTACTGCAGCAGCT
GTTCCTAAAGGCTCCTGTGAACACGGCAGAACTAACAGATCTCTTGATTCAGCAGAACCATGTTGGGAGTGTGATTAAGC
AAACAGACATTTCAGAAGACAGCGATGATGATATGGATGAAGATGAGATTTTCGGCTTCATAAGCCTTTTAAATTTAACC
GAGAGAAAGGGTACTCCATGTGCCGAGCAAATCAAAGAGCTGGTTCTAAGCTGCTGTGAGAAGAGCTGTGAGAAGAGTGT
GGTGGAACAGCTGGACGCGCTCCTGCAGGACGCCAGCAAGCCCGTGGGCTTCCTCCTGAGCGAGAGGCTCATTAACGTCC
CCCCGCAGGTCGCCCTGCCCATGCACCAGCAGCTGCAGAAAGAACTCGCGGAGGCACACAAGACCAATAAGCCGTGTGGG
AAGTGCTGCTTCTACCTGCTGATCAGTAAGACGTTTGTGGAAGCAGGAAAAGGCAGTTCCAAGAAGAAACGGAGCAGCCA
AAAGAAAGAAGAGTTAATGTTTGCAAACGCAGAGGAAGAATTTTTCTATGAGAAGGCAGTCCTGAAGTTCAGCTACTCGG
TGCAGGAGGACAGCGACACCTGTCTGGGAGGCAGATGGTCTTTCGATGATGTGCCCATGAAGCCCATGAGGACTGTGATG
GTGATTCCAGGCGACAAGATGGACGAGATCATGGATAAACTGAAAGAACATCTGTCCGTC

Alignment

ORF - retro_ocun_843 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.62 %
• Parental protein coverage: 82.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QEVNIDFEAYSISDNDYDGIKKLLQQLFLKAPVNTAELTDLLIQQNHVGSVIKQTDISEDSDDDMDEDEI
          .EVNIDFEAYSISDNDYDGIKKLLQQLFLKAPVNTAELTDLLIQQNHVGSVIKQTDISEDSDDDMDEDEI
Retrocopy EEVNIDFEAYSISDNDYDGIKKLLQQLFLKAPVNTAELTDLLIQQNHVGSVIKQTDISEDSDDDMDEDEI

Parental  FGFISLLNLTERKGTPCAEQIKELVLSCCEKSCEKSVVEQLDALLQDASKPVGFLLSERLMNVPPQVALP
          FGFISLLNLTERKGTPCAEQIKELVLS..........VEQLDALLQDASKPVGFLLSERL.NVPPQVALP
Retrocopy FGFISLLNLTERKGTPCAEQIKELVLSXXXXXXXXXXVEQLDALLQDASKPVGFLLSERLINVPPQVALP

Parental  MHQQLQKELAEAHKTSKPCGKCCFYLLISKTFVEAGKGSSKKKRSSQKKEELMFANAEEEFFYEKAVLKF
          MHQQLQKELAEAHKT.KPCGKCCFYLLISKTFVEAGKGSSKKKRSSQKKEELMFANAEEEFFYEKAVLKF
Retrocopy MHQQLQKELAEAHKTNKPCGKCCFYLLISKTFVEAGKGSSKKKRSSQKKEELMFANAEEEFFYEKAVLKF

Parental  SYSVQEDRDTCLGGRWSFDDVPMKPMRTVMVIPGDKMDEIMDKLKEHLSV
          SYSVQED.DTCLGGRWSFDDVPMKPMRTVMVIPGDKMDEIMDKLKEHLSV
Retrocopy SYSVQEDSDTCLGGRWSFDDVPMKPMRTVMVIPGDKMDEIMDKLKEHLSV

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	2.87 RPM	36.37 RPM
SRP017611_kidney	1.93 RPM	29.70 RPM
SRP017611_liver	0.69 RPM	15.41 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_843 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_843 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_843 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012873	1 retrocopy	retro_cfam_1356,
Callithrix jacchus	ENSCJAG00000012411	1 retrocopy	retro_cjac_2838,
Dasypus novemcinctus	ENSDNOG00000002939	1 retrocopy	retro_dnov_530,
Macaca mulatta	ENSMMUG00000008541	1 retrocopy	retro_mmul_472,
Oryctolagus cuniculus	ENSOCUG00000008761	1 retrocopy	retro_ocun_843 ,
Otolemur garnettii	ENSOGAG00000010901	1 retrocopy	retro_ogar_1184,
Ictidomys tridecemlineatus	ENSSTOG00000011828	4 retrocopies	retro_itri_1004, retro_itri_1130, retro_itri_1513, retro_itri_559,
Tupaia belangeri	ENSTBEG00000002570	4 retrocopies	retro_tbel_1259, retro_tbel_1260, retro_tbel_2963, retro_tbel_3044,