RetrogeneDB ID: retro_ocun_1403

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:28478189..28478993(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRPRB
• Ensembl ID: ENSOCUG00000007623
• Aliases: None
• Description: signal recognition particle receptor, B subunit [Source:HGNC Symbol;Acc:24085]

Sequence

>retro_ocun_1403
GCGGACTCCCGGCGGCTGGGGGATGGCGACGGTGCCGGGGGCGCTTTCCAGCCCTATCTAGACTCCTTGCGGCAGGAGCT
GCAGCAGAGGGACCCGACGGTGCTGTCAGTAGTGGTGGCGCTTCTCGCGGTGTTGCTGACGCTGGTGTTCTGGAAGCTCG
TCTGCAGCAGAAGGAGCAGCCAGAGAGCGGTGCTGCTGCTCGGCCTTTGCGACTCCGGAAAGACGTTGCTGTTCGTCAGG
TTGTTAACAGGCCATTACAGAGACACCCAGACGTCCATCACAGATAGCTCTGCCACATACAGAGTCAACAATAATAGGGG
CAATAGTCTGACCTTGATTGACCTCCCTGGCCATGAGAGCTTGCGGCTTCAGTTCTTAGAGCGGTTTAAGACTTCAGCCA
GGGCTGTTGTGTTTGTCGTGGATAGTGCAGCATTTCAGAGAGAGGTAAAAGATGTGGCTGAGTTTCTGTATCAAGTCCTC
ATTGACAGCATGAGTCTGAAGAACACACCATCGTTCCTAATAGCCTGCAACAAGCAAGATATTGCAATGGCAAAATCAGC
AAAGTTAATTCAGCAACAGCTTGAGAAAGAACTTAACACCTTATGAGTTACCCGTTCTGCTGCACCCAGTACACTGGACA
GTTCCAGCACTGCCCCTGCTCAACTGGGAAAGAAAGGCAAAGAATTTGAATTCTCACAGTTGCCCCTCAAAGTGGAGTTC
CTGGAGTGTAGTGCCAAGGGTGGGAGAGGGGACCCCGGCTCCGCTGACATCCAGGACCTGGAGAAGTGGCTTGCTAAAAT
CGCC

Alignment

ORF - retro_ocun_1403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.25 %
• Parental protein coverage: 98.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADSRRLGDGDGAGGAFQPYLDSLRQELQQRDPTVLSVVVALLAVLLTLVFWKLVRSRRSSQRAVLLLGLC
          ADSRRLGDGDGAGGAFQPYLDSLRQELQQRDPTVLSVVVALLAVLLTLVFWKLV.SRRSSQRAVLLLGLC
Retrocopy ADSRRLGDGDGAGGAFQPYLDSLRQELQQRDPTVLSVVVALLAVLLTLVFWKLVCSRRSSQRAVLLLGLC

Parental  DSGKTLLFVRLLTGHYRDTQTSITDSSATYRVNNNRGNSLTLIDLPGHESLRLQFLERFKTSARAVVFVV
          DSGKTLLFVRLLTGHYRDTQTSITDSSATYRVNNNRGNSLTLIDLPGHESLRLQFLERFKTSARAVVFVV
Retrocopy DSGKTLLFVRLLTGHYRDTQTSITDSSATYRVNNNRGNSLTLIDLPGHESLRLQFLERFKTSARAVVFVV

Parental  DSAAFQREVKDVAEFLYQVLIDSMSLKNTPSFLIACNKQDIAMAKSAKLIQQQLEKELNTLRVTRSAAPS
          DSAAFQREVKDVAEFLYQVLIDSMSLKNTPSFLIACNKQDIAMAKSAKLIQQQLEKELNTL.VTRSAAPS
Retrocopy DSAAFQREVKDVAEFLYQVLIDSMSLKNTPSFLIACNKQDIAMAKSAKLIQQQLEKELNTL*VTRSAAPS

Parental  TLDSSSTAPAQLGKKGKEFEFSQLPLKVEFLECSAKGGRGDPGSADIQDLEKWLAKIA
          TLDSSSTAPAQLGKKGKEFEFSQLPLKVEFLECSAKGGRGDPGSADIQDLEKWLAKIA
Retrocopy TLDSSSTAPAQLGKKGKEFEFSQLPLKVEFLECSAKGGRGDPGSADIQDLEKWLAKIA

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	2.76 RPM	17.38 RPM
SRP017611_kidney	3.65 RPM	25.44 RPM
SRP017611_liver	1.16 RPM	11.25 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1403 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1403 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1403 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000009618	1 retrocopy	retro_mmur_505,
Oryctolagus cuniculus	ENSOCUG00000007623	1 retrocopy	retro_ocun_1403 ,