RetrogeneDB ID: retro_ocun_1504

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:41229752..41230249(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCL7A
• Ensembl ID: ENSOCUG00000000630
• Aliases: None
• Description: B-cell CLL/lymphoma 7A [Source:HGNC Symbol;Acc:1004]

Sequence

>retro_ocun_1504
AATATCAGAGGGATCATGGCGGCTATGGAGGAAGTGCACTAAGGGGAGAAGTGAGTGACCCTTGGTGACACGTCCCTACG
AATCTACAAGTGGGTCCCTGCGACAGAGCCGAAGGTTGACGATAAAAACAAGAAGGAGAAAAAAAGGCAAAGATGAGACA
TGTGGCTCGGGGGTGACCGCTCCAGAGAACAGCTCCTTGGCAGGGATGATGGCCATGCAGGAGGACAAGAGCAAACAGAG
TGCCACAGCGGACGCCTCCCTATCAAGCAGATCAGCAGCGGCCCGAGCCTGGCCCCTGGGGCCCAGCTTCACCGTGCCCA
GTGACTGCACGGAAGCCCTGGTCGGGTGAGGCGCCGGCCGACCGAAAGGTCCATCCTGGGGTTAAGGATCAGAATTCTCA
GTCTCCGGTGGAAAAGGCCCTGAACAACAGTTCCGAGAAAACAGAATGGCGACCTTCTAGGGACTCGGCTCTGGCTGAAG
GGGCAGCAGCAATCGCA

Alignment

ORF - retro_ocun_1504 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.14 %
• Parental protein coverage: 80.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DIKRVMAAIEKVRKWEKKWVTVGDTSLRIYKWVPVTEPKVDEKNKN-KKKGKDEKCGSEVTTPENSSSPG
          .I...MAA.E.V...EK..VT.GDTSLRIYKWVP.TEPKVD.KNK...KKGKDE.CGS.VT.PENSS..G
Retrocopy NIRGIMAAMEEVH*GEK*-VTLGDTSLRIYKWVPATEPKVDDKNKK>RKKGKDETCGSGVTAPENSSLAG

Parental  MMDMHDDNSNQSSIADAS-PIKQENSSNSSPAP-EPSSAVPGDGPEAK-ADEAQADGKEHPGTEDASDEQ
          MM.M..D.S.QS..ADAS.PIKQ..SS..S.AP..PS..VP.D..EA....EA.AD.K.HPG..D....Q
Retrocopy MMAMQEDKSKQSATADAS<PIKQ-ISSGPSLAP>GPSFTVPSDCTEAL>SGEAPADRKVHPGVKD----Q

Parental  NSQSPVENAM-NSSEKGERQPSGDSGLAAESSAIS
          NSQSPVE.A..NSSEK.E..PS.DS.LA....AI.
Retrocopy NSQSPVEKALNNSSEKTEWRPSRDSALAEGAAAIA

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	36.42 RPM
SRP017611_kidney	0.00 RPM	30.81 RPM
SRP017611_liver	0.00 RPM	7.63 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1504 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1504 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1504 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013429	1 retrocopy	retro_dnov_1682,
Loxodonta africana	ENSLAFG00000007425	1 retrocopy	retro_lafr_617,
Macropus eugenii	ENSMEUG00000013687	2 retrocopies	retro_meug_1658, retro_meug_611,
Oryctolagus cuniculus	ENSOCUG00000000630	1 retrocopy	retro_ocun_1504 ,