RetrogeneDB ID: retro_ocun_980

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 18:56052067..56053375(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STK4
• Ensembl ID: ENSOCUG00000003016
• Aliases: None
• Description: serine/threonine kinase 4 [Source:HGNC Symbol;Acc:11408]

Sequence

>retro_ocun_980
ATGGAGACGGTACAGCTGAGGAACCGCCCGCCGGCAGCTGAAAAAGTTGGATGAAGACAGTTTAACCAAACAACCAGAAG
TATTTGATGTCTTGGAGAAACTCGGAGAAGGGTCCTATGGCAGCAAGTATAAAGCTTTTCATAAAGAGACCAGACAGATT
GTGGCTATTAAACAAGTTCCTGTCGAATCAGATCTTCAGGAGGTAATCAAAGAAATCTCCATAATGCAGCAATGTGACAG
CCCTCATGTAGTCAAATACTATGGAAGTTATTTTAAGAACACAGACTTATGGATCATTATGGAGTACTGTGGAGCTGGCT
CTGTATCTGATCTCATTCGATTACGAAATAAAACGTTAACAGAAGATGAAATAACTACAGTATTACAATCAACTCTTAAA
GGATTGGAATACCTTTATTTTATGAGAAAAATACACCGAGATATCAAGGCAGGAAATATTTTGTTAAATACAGAGGGACA
TGCAAAACTCTCAGATTTTGGTGTAACAGGTCAGCTTACAGATACCATGGCCAGCGCAATACAGTAATAGGAACACCATT
TTGGATGGCTCCAGAGGTGATTCAGGAAATTGGGTACAACTGTGTGGCAGACAGCTGGTCTCTGGGAATAACTGCCATAG
AAATGGCTGAAGGAAAGCCACCATATGCTGATATCCATCCCATGAGGGCAATCTTCATGATTCCTACAAACCCTCCGCCC
ATGTTCCGAAAACCAGAGCTGTGGTCAGATAACTTTACAGACTTTGTGAAGCAGTGTCTTGTAAAGAGCCCTGAGCAGAG
GGCCACAGCCACTCAGCTCCTATAGCACCCGCTTGTCAGGAATGTTAAAGGAGTGTCAATGTTGCGGGACTTAATTAAGG
AAGCCATGGATGTGAAACTGAAACGCCAGGAATCCCAGCAGCGGGAAGTGGACCAAGACGATGAAGATAACTCAGAGGAG
GATGAAATGGATTCTGGCATGATGGTTCGTGCAGCGGGCGATGAGATGGGCACTGTGCGTGTGGCCAGCACCATGAGTGA
TGGAGCCAATACCATGATTGAGCATGAAGACACCTTGCCCTCACAGCTGGGCACCATGGTGATCAATGCAGAGGATGAGG
AAGAGGAAGGGGCGATGAAAAGAAGGGACGAGACTATGCAGCCTGTAAAACCATCTTTCCTTGAATACTTTGAACAAAAA
GAAAAGGAAAACCAGGTCAACAGCTTTGGCAAGAGTGTACCTGCTCCACTGAAAAATTCTTCCGATTGGGAAGTACCACT
GGATGGAGACTGTGAGTTTGTAAGTAGT

Alignment

ORF - retro_ocun_980 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.65 %
• Parental protein coverage: 89.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  METVQLRN-PP-RRQLKKLDEDSLTKQPEEVFDVLEKLGEGSYGSVYKAIHKETGQIVAIKQVPVESDLQ
          METVQLRN.PP.RRQLKKLDEDSLTKQPE.VFDVLEKLGEGSYGS.YKA.HKET.QIVAIKQVPVESDLQ
Retrocopy METVQLRN<PP<RRQLKKLDEDSLTKQPE-VFDVLEKLGEGSYGSKYKAFHKETRQIVAIKQVPVESDLQ

Parental  EIIKEISIMQQCDSPHVVKYYGSYFKNTDLWIVMEYCGAGSVSDIIRLRNKTLTEDEIATVLQSTLKGLE
          E.IKEISIMQQCDSPHVVKYYGSYFKNTDLWI.MEYCGAGSVSD.IRLRNKTLTEDEI.TVLQSTLKGLE
Retrocopy EVIKEISIMQQCDSPHVVKYYGSYFKNTDLWIIMEYCGAGSVSDLIRLRNKTLTEDEITTVLQSTLKGLE

Parental  YLHFMRKIHRDIKAGNILLNTEGHAKLADFGVAGQLTDTMA-KRNTVIGTPFWMAPEVIQEIGYNCVADI
          YL.FMRKIHRDIKAGNILLNTEGHAKL.DFGV.GQLTDTMA..RNTVIGTPFWMAPEVIQEIGYNCVAD.
Retrocopy YLYFMRKIHRDIKAGNILLNTEGHAKLSDFGVTGQLTDTMA<QRNTVIGTPFWMAPEVIQEIGYNCVADS

Parental  WSLGITAIEMAEGKPPYADIHPMRAIFMIPTNPPPTFRKPELWSDNFTDFVKQCLVKSPEQRATATQLLQ
          WSLGITAIEMAEGKPPYADIHPMRAIFMIPTNPPP.FRKPELWSDNFTDFVKQCLVKSPEQRATATQLL.
Retrocopy WSLGITAIEMAEGKPPYADIHPMRAIFMIPTNPPPMFRKPELWSDNFTDFVKQCLVKSPEQRATATQLL*

Parental  HPFVRNAKGVSMLRDLINEAMDVKLKRQESQQREVDQDDEDNSEEDEMDSGTMVRAAGDEMGTVRVASTM
          HP.VRN.KGVSMLRDLI.EAMDVKLKRQESQQREVDQDDEDNSEEDEMDSG.MVRAAGDEMGTVRVASTM
Retrocopy HPLVRNVKGVSMLRDLIKEAMDVKLKRQESQQREVDQDDEDNSEEDEMDSGMMVRAAGDEMGTVRVASTM

Parental  SDGASTMIEHEDTLPSQLGTMVINAEDEEEEGTMKRRDETMQPVKPSFLEYFEQKEKENQVNSFGKSVPA
          SDGA.TMIEHEDTLPSQLGTMVINAEDEEEEG.MKRRDETMQPVKPSFLEYFEQKEKENQVNSFGKSVPA
Retrocopy SDGANTMIEHEDTLPSQLGTMVINAEDEEEEGAMKRRDETMQPVKPSFLEYFEQKEKENQVNSFGKSVPA

Parental  PLKNSSDWKVPLDGDYEFLKS
          PLKNSSDW.VPLDGD.EF..S
Retrocopy PLKNSSDWEVPLDGDCEFVSS

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	0.11 RPM	7.56 RPM
SRP017611_kidney	0.20 RPM	15.71 RPM
SRP017611_liver	0.08 RPM	6.47 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_980 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_980 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_980 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ornithorhynchus anatinus	ENSOANG00000013669	1 retrocopy	retro_oana_65,
Oryctolagus cuniculus	ENSOCUG00000003016	2 retrocopies	retro_ocun_1122, retro_ocun_980 ,