RetrogeneDB ID: retro_ocun_1626

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018723:2105837..2106371(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000003932
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CNBP
• Ensembl ID: ENSOCUG00000008696
• Aliases: None
• Description: CCHC-type zinc finger, nucleic acid binding protein [Source:HGNC Symbol;Acc:13164]

Sequence

>retro_ocun_1626
ATGAGCAGCAATGAGTGCTTCAAATGTGGACGATCTGGCCACTGGGCCCGGGAATGCCCTACTGGTGGAGGCCGTGGTCG
TGGAATGAGAAGCCGCGGCAGAGGTGGTTTTACCTCGGATAGAGGTTTCCAGTTTGTTTCCTCATCTCTTCCAGACATCT
GTTACCGCTGTGGTGAGTCTGGCCATCTTGCCAAGGATTGTGATCTTCAGGAGGATGAAGCCTGCTATAACTGCGGTAGA
GGTGGCCACATTGCCAAGGACTGCAAGGAGCCCAAGAGAGAGCGAGAGCAATGCTGCTACAACTGTGGCAAACCAGGCCA
TCTGGCTCGTGACTGTGACCATGCCGATGAGCAGAAGTGCTATTCTTGTGGAGAATTTGGACACATTCAAAAAGACTGCA
CCAAGGTGAAGTGCTATAGGTGTGGTGAAACTGGTCATGTAGCCATCAACTGCAGCAAGACAAGTGAAGTCAACTGTTAC
CGCTGTGGCGAGTCAGGGCACCTTGCACGGGAATGCACGATCGAGGCTACAGCC

Alignment

ORF - retro_ocun_1626 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.44 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSNECFKCGRSGHWARECPTGGGRGRGMRSRGRGGFTSDRGFQFVSSSLPDICYRCGESGHLAKDCDLQ
          MSSNECFKCGRSGHWARECPTGGGRGRGMRSRGRGGFTSDRGFQFVSSSLPDICYRCGESGHLAKDCDLQ
Retrocopy MSSNECFKCGRSGHWARECPTGGGRGRGMRSRGRGGFTSDRGFQFVSSSLPDICYRCGESGHLAKDCDLQ

Parental  ED-ACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDHADEQKCYSCGEFGHIQKDCTKVKCYR
          ED.ACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDHADEQKCYSCGEFGHIQKDCTKVKCYR
Retrocopy EDEACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDHADEQKCYSCGEFGHIQKDCTKVKCYR

Parental  CGETGHVAINCSKTSEVNCYRCGESGHLARECTIEATA
          CGETGHVAINCSKTSEVNCYRCGESGHLARECTIEATA
Retrocopy CGETGHVAINCSKTSEVNCYRCGESGHLARECTIEATA

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	8.44 RPM	20.14 RPM
SRP017611_kidney	9.93 RPM	19.16 RPM
SRP017611_liver	8.48 RPM	15.49 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1626 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1626 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1626 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012159	1 retrocopy	retro_btau_19,
Callithrix jacchus	ENSCJAG00000017430	1 retrocopy	retro_cjac_4079,
Equus caballus	ENSECAG00000009512	1 retrocopy	retro_ecab_1072,
Echinops telfairi	ENSETEG00000008408	5 retrocopies	retro_etel_12, retro_etel_1791, retro_etel_2192, retro_etel_237, retro_etel_583,
Felis catus	ENSFCAG00000028042	2 retrocopies	retro_fcat_1922, retro_fcat_2001,
Loxodonta africana	ENSLAFG00000002502	1 retrocopy	retro_lafr_49,
Oryctolagus cuniculus	ENSOCUG00000008696	2 retrocopies	retro_ocun_1626 , retro_ocun_208,
Otolemur garnettii	ENSOGAG00000013898	1 retrocopy	retro_ogar_144,
Pteropus vampyrus	ENSPVAG00000015070	1 retrocopy	retro_pvam_908,
Sorex araneus	ENSSARG00000011874	1 retrocopy	retro_sara_397,
Sarcophilus harrisii	ENSSHAG00000017132	1 retrocopy	retro_shar_666,