RetrogeneDB ID: retro_ocun_405

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:152835821..152836956(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000027743
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SCLY
• Ensembl ID: ENSOCUG00000002777
• Aliases: None
• Description: selenocysteine lyase [Source:HGNC Symbol;Acc:18161]

Sequence

>retro_ocun_405
GGTCGGAAGGCCAAGGACATTATAAACGCAGCGCGGGAAAACGTGGCGAAGATGATAGGTGCGAAACCTCGAGACATAGT
CTTCACCTCCGGGGGGACTGAGTCAAACAACTTAGTGATCCATTCTGCGATGAAAACCTTCCACGAAAACGAAGCCTCCG
GAGGGGGCGCGGTGGAGCACCCCAGCCCGGTAGAGGGGGCCACGCCCCACTTCGTAACGAGCACAGTGGAGCACGACTCC
ATCTCTCTGCCCCTGCAGCACCTGGCAAAGGAGCAAGTGGCCGCAGTCACCTTTGTCCCAGTGTCCAAGGTGAGCGGGCA
GGTGGAGGTAGACGACGTCCTGGCCGCAGTCCGTCCCACCACGTGCCTGGTGACCATCATGCTGGCCAATAACGAGACTG
GCATCATCATGCCTGTCCCCGAAATCAGCCAGCGCATCGCAGCCCTGAACCAGAAGCGGGCAGCGTCCGGGCTGCCCCGC
GTCCTGCGGCACACGGACGCCGCGCAGGCGTTGGGGAAGAGGCGCGTGGATGTGGAGGACCTGGGTGTGGACTTCCTGAC
CATCGTGGGGCACAAGTTCTACGGCCCCAGGATTGGCGCGCTTTATGTTCGAGGGCTCGGTGAACTCACCCCTCTGTACC
CCATGCTGTTTGGAGGTGGACAAGAGCGGAATTTCAGGCCAGGGACGGAGAACACCCCGATGATTGCCGGCCTTGGGAAG
GCTGCTGAGCTGGTGACCGCGAACTGTGAGGCTTACGAGGCCCACATGAGAGACGTCTGAGACTACCTGGAGGAGAGGCT
GGAGGCTGAGTTTGGTAAAAAGAGAATCCATCTCAATAACCGGTTTCCAGGGGCCGAGCGGCTGCCAAACACCTGTAACG
TTTCCATCCGGGGACCCCAGCTTCCAGGCCGCCTGGTGCTCGCACAGTGCCGGACGCTGCTGGCCAGCGTAGAGGCCACA
TGCCACTCGGACCTCGGGGACCAGCCGTCGCCCGTGCTGCTGAGCTGCGGCGTCCCCTTCGCGGTGGCCAAGAACGCGCT
GTGCCTCAGCGTGGGCCGCAGCACCACCAGGGCAGAGGTGGAGCTCGCCGTGCAGGACCTGAAGCAGGCCGTTGGCCCGG
CTGGAGGGCCAGGCC

Alignment

ORF - retro_ocun_405 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.1 %
• Parental protein coverage: 91.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRKAKDIINAARENVAKMIGANPRDIVFTSGGTESNNLVIHSAMKTFHENKASGGGALEHPSPVEGATPH
          GRKAKDIINAARENVAKMIGA.PRDIVFTSGGTESNNLVIHSAMKTFHEN.ASGGGA.EHPSPVEGATPH
Retrocopy GRKAKDIINAARENVAKMIGAKPRDIVFTSGGTESNNLVIHSAMKTFHENEASGGGAVEHPSPVEGATPH

Parental  FVTSTVEHDSISLPLQHLAKEQVAAVTFVPVSKVSGQVEVDDVLAAVRPTTCLVTIMLANNETGIIMPVP
          FVTSTVEHDSISLPLQHLAKEQVAAVTFVPVSKVSGQVEVDDVLAAVRPTTCLVTIMLANNETGIIMPVP
Retrocopy FVTSTVEHDSISLPLQHLAKEQVAAVTFVPVSKVSGQVEVDDVLAAVRPTTCLVTIMLANNETGIIMPVP

Parental  EISQRIAALNQKRAVSGLPRVLLHTDAAQALGKRRVDVEDLGVDFLTIVGHKFYGPRIGALYVRGLGDLT
          EISQRIAALNQKRA.SGLPRVL.HTDAAQALGKRRVDVEDLGVDFLTIVGHKFYGPRIGALYVRGLG.LT
Retrocopy EISQRIAALNQKRAASGLPRVLRHTDAAQALGKRRVDVEDLGVDFLTIVGHKFYGPRIGALYVRGLGELT

Parental  PLYPMLFGGGQERNFRPGTENTPMIAGLGKAAELVTANCEAYEAHMRDVRDYLEERLEAEFGKKRIHLNN
          PLYPMLFGGGQERNFRPGTENTPMIAGLGKAAELVTANCEAYEAHMRDV.DYLEERLEAEFGKKRIHLNN
Retrocopy PLYPMLFGGGQERNFRPGTENTPMIAGLGKAAELVTANCEAYEAHMRDV*DYLEERLEAEFGKKRIHLNN

Parental  RFPGAERLPNTCNVSIRGPQLPGRLVLAQCRTLLASVGAACHSDLGDQPSPVLLSCGVPFAVAKNALRLS
          RFPGAERLPNTCNVSIRGPQLPGRLVLAQCRTLLASV.A.CHSDLGDQPSPVLLSCGVPFAVAKNAL.LS
Retrocopy RFPGAERLPNTCNVSIRGPQLPGRLVLAQCRTLLASVEATCHSDLGDQPSPVLLSCGVPFAVAKNALCLS

Parental  VGRSTTRAEVELAVQDLKQAV-ARLEGQA
          VGRSTTRAEVELAVQDLKQAV.ARLEGQA
Retrocopy VGRSTTRAEVELAVQDLKQAV>ARLEGQA

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	1.49 RPM	36.76 RPM
SRP017611_kidney	1.82 RPM	45.00 RPM
SRP017611_liver	0.69 RPM	52.26 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_405 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_405 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_405 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013824	2 retrocopies	retro_chof_1528, retro_chof_1707,
Callithrix jacchus	ENSCJAG00000000471	1 retrocopy	retro_cjac_3989,
Oryctolagus cuniculus	ENSOCUG00000002777	1 retrocopy	retro_ocun_405 ,
Oryctolagus cuniculus	ENSOCUG00000017050	1 retrocopy	retro_ocun_1214,
Tarsius syrichta	ENSTSYG00000002756	1 retrocopy	retro_tsyr_1779,