RetrogeneDB ID: retro_ocun_710

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:88981240..88982569(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRD2
• Ensembl ID: ENSOCUG00000003097
• Aliases: None
• Description: bromodomain containing 2 [Source:HGNC Symbol;Acc:1103]

Sequence

>retro_ocun_710
ATGTTGCAAAACGTGACTCCCCACAACAAGCTCCCTGGGGAAGGGAATGCAGGGTTACTGGGGCTGGGTCCAGAGGCGGC
AGCACCAGGGAAAAGGATTCGAAAGCCCTCCCTGTTGTATGAGGGATTTGAAAGCCCTACGATGGCTTCAGTGCCGGCTT
TGCAACTGACCCCTGCCAACCCACCACCCCCGGAGGTGTCTAATCCCAAAAAGCCAGGACGAGTCACCAATCAGCTTCAG
TACCTGCACAAGGTGGTGATGAAGGCTCTATGGAAACATCAGTTTGCCTGGCCATTCCGGCAGCCTGTGGATGCTGTCAA
ATTGGGCCTTCCGGACTATCACAAAATTATAAAACAGCCTATGGATATGGGTACTATTAAGAGGAGACTTGAAAACAATT
ACTATTGGGCTGCCTCCGAGTGTATGCAGGATTTCAATACTATGTTCACCAACTGTTACATTTACAACAAGCCCACTGAT
GACATTGTCTTGATGGCACAAACACTGGAAAAGATCTTCCTACAGAAAGTGGCGTCAATGCCCCAAGAAGAGCAAGAGCT
CGTGGTGACCATCCCTAAGAACAGCCACAAAAAGGGGGCCAAGCTGGCAGCACTATAGGGCAGTATTACCAGTGCCCATC
AGGTGCCTGCCGTCTCTTCTGTGTCCCACACAGCCCTGTATACTCCACCGCCTGAGATACCTACCACCGTCCTCAACATT
CCCCATCCGTCAGTCATCTCTTCTCCCCTTCTCAAGTCCCTGCACTCTGCTGGCCCTCCGCTCCTTGCTGTCTCCGCAGC
TCCTCCAGCTCAGCCTCTTGCCAAGAAAAAAGGGGTTAAGCGGAAAGCAGATACTACCACCCCTACACCTACGGCCATCC
TGGCTCCTGGTTCTCCAGCTAGCCCTCCTGGGGGTCTTGAACCTAAGGCAGCAAGGCTTCCGCCTATGCGCAGAGAGAGT
GGCCGCCCCATCAAGCCCCCACGCAAAGATTTGCCTGACTCTCAGCAGCAACACCAGAGCTCTAAGAAAGGAAAGCTCTC
CGAACAGTTAAAACATTGCAATGGCATCTTGAAGGAGCTACTCTCTAAGAAGCATGCTGCCTATGCCTGGCCTTTCTATA
AACCCGTGGACGCTTCTGCTCTCGGCCTGCATGACTACCATGACATCATTAAGCACCCCATGGACCTCAGCACTGTCAAG
CGGAAGATGGAGAATCGTGATTACCGAGATGCACAGGAGTTTGCTGCTGATGTGCGGCTTATGTTCTCCAACTGCTACAA
GTACAATCCTCCCGATCATGATATTGTGGCCATGGCCCGAAAGCTACAG

Alignment

ORF - retro_ocun_710 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.55 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLQNVTPHNKLPGEGNAGLLGLGPEAAAPGKRIRKPSLLYEGFESPTMASVPALQLTPANPPPPEVSNPK
          MLQNVTPHNKLPGEGNAGLLGLGPEAAAPGKRIRKPSLLYEGFESPTMASVPALQLTPANPPPPEVSNPK
Retrocopy MLQNVTPHNKLPGEGNAGLLGLGPEAAAPGKRIRKPSLLYEGFESPTMASVPALQLTPANPPPPEVSNPK

Parental  KPGRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASE
          KPGRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASE
Retrocopy KPGRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASE

Parental  CMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQEEQELVVTIPKNSHKKGAKLAALQGSIT
          CMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQEEQELVVTIPKNSHKKGAKLAAL.GSIT
Retrocopy CMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQEEQELVVTIPKNSHKKGAKLAAL*GSIT

Parental  SAHQVPAVSSVSHTALYTPPPEIPTTVLNIPHPSVISSPLLKSLHSAGPPLLAVSAAPPAQPLAKKKGVK
          SAHQVPAVSSVSHTALYTPPPEIPTTVLNIPHPSVISSPLLKSLHSAGPPLLAVSAAPPAQPLAKKKGVK
Retrocopy SAHQVPAVSSVSHTALYTPPPEIPTTVLNIPHPSVISSPLLKSLHSAGPPLLAVSAAPPAQPLAKKKGVK

Parental  RKADTTTPTPTAILAPGSPASPPGGLEPKAARLPPMRRESGRPIKPPRKDLPDSQQQHQSSKKGKLSEQL
          RKADTTTPTPTAILAPGSPASPPGGLEPKAARLPPMRRESGRPIKPPRKDLPDSQQQHQSSKKGKLSEQL
Retrocopy RKADTTTPTPTAILAPGSPASPPGGLEPKAARLPPMRRESGRPIKPPRKDLPDSQQQHQSSKKGKLSEQL

Parental  KHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRL
          KHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRL
Retrocopy KHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRL

Parental  MFSNCYKYNPPDHDVVAMARKLQ
          MFSNCYKYNPPDHD.VAMARKLQ
Retrocopy MFSNCYKYNPPDHDIVAMARKLQ

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	6.02 RPM	47.41 RPM
SRP017611_kidney	6.28 RPM	51.29 RPM
SRP017611_liver	4.62 RPM	28.44 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_710 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_710 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_710 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021566	2 retrocopies	retro_cjac_2409, retro_cjac_564,
Oryctolagus cuniculus	ENSOCUG00000003097	1 retrocopy	retro_ocun_710 ,