RetrogeneDB ID: retro_ocun_1724

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018825:361073..362009(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUPT3H
• Ensembl ID: ENSOCUG00000014574
• Aliases: None
• Description: suppressor of Ty 3 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:11466]

Sequence

>retro_ocun_1724
GCAGCTAGCCCAATGTATACTGCCACTTCAAATAGTGAAAGAGGTACAGGGAAGTCTATAAGCTTCATGGCAGAAATAAA
GAGTATGATGTTTTCTTTGGGTGATGCCAGGAGGCCTCTTCATGAAACAGCAGTTTTGGTAGAAGATGTGGAGCATACTC
AGTTAATTAATCTGTTATGGCAAGCTGCTGAAGTTTCTCAGCTGCGGGGAGCAAGGGTAGTTTCTCCTGAAGATATTCTG
TTTTTGATGTGCAAAGATAAGAAAAAACTTAGAAGACTGTTAAAATACATGTTTATGCGAGACTACAAATCAAAGATTAT
CAAAAGCATAGATGATGATGATCTTCGAGAAAACAAATTGAGTGGCAGCAGTAAAACAAACAAAAGACAAAAAATTGCTC
AAGACTTCTTCAACTCTATTGACCAGACTGGAGAACTAATGGCAATGCTTGAAAATGACGAAATTGATGAAGTTAAACAA
GAAAGAATGGAGAGAGCAGAAAGACAAACTCAAATTATGGATTCAGCTCAATATGCAGAATTCTGTAAAAGTCAACATTT
AAGTTTCTCCAAGAAAAGTTCCAAATTTTGAAACTGGTTGGACTGCTGCAGTATGGAGATAAAGCCCACTATTGTTGCTA
TGGAAATTTTAGCAGATTTAGCATATGAAACTGTGGCACAGCTGGTGGATTTGGCTCTTGTGAGACAGGACATGGTAACC
AAGGCAGGGGACCCCTTCAGTCATGCCATTTCTGCAAACTTCATGCAGTATCACAGCTCTGCTGAGAGCGCTGCAGCCTG
TGGTGTTGAGGCTCACAGCAATGCTATCCAGCCCTGCCACATCAGAGAAGCTGTTTGATGCTATGGCCACAAGATTGGTC
CCCTTTCCCCATTCACAAGTGCCTACCACAGGAGTGGGATGGCTTTTCTACCCTGC

Alignment

ORF - retro_ocun_1724 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.14 %
• Parental protein coverage: 98.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AASPMSTATSNSGRSTGKSISFVAELQSMMFSLGDARRPLHETVVLVEDVVHTQLINLLQQAAEVSQLRG
          AASPM.TATSNS.R.TGKSISF.AE..SMMFSLGDARRPLHET.VLVEDV.HTQLINLL.QAAEVSQLRG
Retrocopy AASPMYTATSNSERGTGKSISFMAEIKSMMFSLGDARRPLHETAVLVEDVEHTQLINLLWQAAEVSQLRG

Parental  ARVISPEDLLFLMRKDKKKLRRLLKYMFMRDYKSKIIKSIDEDDLLEDKLSGSSNTNKRQKIAQDFFNSI
          ARV.SPED.LFLM.KDKKKLRRLLKYMFMRDYKSKIIKSID.DDL.E.KLSGSS.TNKRQKIAQDFFNSI
Retrocopy ARVVSPEDILFLMCKDKKKLRRLLKYMFMRDYKSKIIKSIDDDDLRENKLSGSSKTNKRQKIAQDFFNSI

Parental  DQTGELMAMLENDEIDEVKQERMERAERQTRIMDSAQYAEFCESRHLSFSKKTSKFRDWLDCSSMEIKPT
          DQTGELMAMLENDEIDEVKQERMERAERQT.IMDSAQYAEFC.S.HLSFSKK.SKF..WLDC.SMEIKPT
Retrocopy DQTGELMAMLENDEIDEVKQERMERAERQTQIMDSAQYAEFCKSQHLSFSKKSSKF*NWLDCCSMEIKPT

Parental  IVAMEILAYLAYETVAQLVDLALLVRQDMVTKAGDPFSHAMSAAFIQYHNSAESAAACGVEAHSDAIQPC
          IVAMEILA.LAYETVAQLVDLA.LVRQDMVTKAGDPFSHA.SA.F.QYH.SAESAAACGVEAHS.AIQPC
Retrocopy IVAMEILADLAYETVAQLVDLA-LVRQDMVTKAGDPFSHAISANFMQYHSSAESAAACGVEAHSNAIQPC

Parental  HIREAVRRYGHKIGPLSPFTSAYRRSGMAFLAC
          HIREAV..YGHKIGPLSPFTSAY.RSGMAFL.C
Retrocopy HIREAV*CYGHKIGPLSPFTSAYHRSGMAFLPC

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	6.40 RPM
SRP017611_kidney	0.00 RPM	6.79 RPM
SRP017611_liver	0.00 RPM	4.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1724 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1724 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1724 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000024037	1 retrocopy	retro_cpor_1320,
Dasypus novemcinctus	ENSDNOG00000011043	1 retrocopy	retro_dnov_150,
Echinops telfairi	ENSETEG00000004704	1 retrocopy	retro_etel_1029,
Myotis lucifugus	ENSMLUG00000016339	1 retrocopy	retro_mluc_2262,
Oryctolagus cuniculus	ENSOCUG00000014574	1 retrocopy	retro_ocun_1724 ,