RetrogeneDB ID: retro_ocun_56

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:69407800..69408250(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000008012
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000006493
• Aliases: None
• Description: Stathmin [Source:UniProtKB/TrEMBL;Acc:G1SR41]

Sequence

>retro_ocun_56
ATGGCGTCTTCTGATATTCAGGTGAAAGAACTGGAGAAGCGTGCTTCGGGCCAGGCTTTTGAGCTGATTCTCAGCCCTCG
GTCAAAAGAATCTGTCCCGGATTTCCCCCTTTCCCCTCCGAAGAAGAAGGATCTTTCCCTGGAGGAGATTCAGAAGAAAT
TAGAAGCTGCTGAAGAAAGACGCAAGTCCCATGAAGCCGAGGTCTTGAAGCAGCTTGCCGAGAAACGGGAGCACGAGAAA
GAAGTGCTGCAGAAAGCGATAGAAGAGAACAACAACTTCAGCAAAATGGCGGAAGAGAAACTGACCCACAAGATGGAAGC
TAACAAAGAGAACCGGGAGGCCCAGATGGCTGCCAAGCTGGAGCGTTTGCGAGAGAAGGATAAGCACATTGAGGAAGTGC
GGAAGAACAAAGAATCCAAAGACCCCGCTGATGAGACTGAAGCTGACTAA

Alignment

ORF - retro_ocun_56 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STADIQVKELEKRASGQAFELILSPRSKESVPDFPLSPPKKKDLSLEEIQKKLEAAEERRKSHEAEVLKQ
          ...DIQVKELEKRASGQAFELILSPRSKESVPDFPLSPPKKKDLSLEEIQKKLEAAEERRKSHEAEVLKQ
Retrocopy ASSDIQVKELEKRASGQAFELILSPRSKESVPDFPLSPPKKKDLSLEEIQKKLEAAEERRKSHEAEVLKQ

Parental  LAEKREHEKEVLQKAIEENNNFSKMAEEKLTHKMEANKENREAQMAAKLERLREKDKHIEEVRKNKESKD
          LAEKREHEKEVLQKAIEENNNFSKMAEEKLTHKMEANKENREAQMAAKLERLREKDKHIEEVRKNKESKD
Retrocopy LAEKREHEKEVLQKAIEENNNFSKMAEEKLTHKMEANKENREAQMAAKLERLREKDKHIEEVRKNKESKD

Parental  PADETEAD
          PADETEAD
Retrocopy PADETEAD

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	40.84 RPM	186.65 RPM
SRP017611_kidney	0.91 RPM	4.36 RPM
SRP017611_liver	0.08 RPM	0.46 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_56 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_56 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_56 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013761	1 retrocopy	retro_btau_247,
Callithrix jacchus	ENSCJAG00000009462	2 retrocopies	retro_cjac_3206, retro_cjac_474,
Cavia porcellus	ENSCPOG00000011075	1 retrocopy	retro_cpor_1505,
Equus caballus	ENSECAG00000021662	1 retrocopy	retro_ecab_490,
Loxodonta africana	ENSLAFG00000006089	1 retrocopy	retro_lafr_84,
Mustela putorius furo	ENSMPUG00000015774	1 retrocopy	retro_mputfur_1191,
Mus musculus	ENSMUSG00000028832	3 retrocopies	retro_mmus_1660, retro_mmus_2470, retro_mmus_3383,
Oryctolagus cuniculus	ENSOCUG00000006493	1 retrocopy	retro_ocun_56 ,
Pteropus vampyrus	ENSPVAG00000006344	1 retrocopy	retro_pvam_53,
Rattus norvegicus	ENSRNOG00000016810	4 retrocopies	retro_rnor_1604, retro_rnor_1855, retro_rnor_2048, retro_rnor_765,
Sorex araneus	ENSSARG00000011057	2 retrocopies	retro_sara_271, retro_sara_764,
Sarcophilus harrisii	ENSSHAG00000006382	1 retrocopy	retro_shar_391,
Ictidomys tridecemlineatus	ENSSTOG00000021708	5 retrocopies	retro_itri_1806, retro_itri_1833, retro_itri_554, retro_itri_819, retro_itri_826,