RetrogeneDB ID: retro_ocun_1122

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:146414462..146415898(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023200
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1122
CCTGGTGCTTGGCAGCTGAAAATGTTGGATGAAGACAGTTTAACCAAACAACCAGAAGAAGTATCTGATGTCTTGGAGAA
ACTTGGAGAAAGGTCCTATGGCAGCGTGTATAAAGCTATTCATAAAGAGACTGGACAGATTGTGGCTATTAAGCAAGTTC
CTGTAGAATCAGACCTTCAGGAGATAATCAAAGAAATCTCCATAATGCAGCAATGTGACAGCCCTCATGTAGTCAAATAT
TATGGAAGTTATTTTAAGAACACAGACTTATGGATTGTTATGGAGTACTGTGGAGCTGGCTCTGTATCTGATATCATTCG
ATTACAAAATAAAACGTTAACAGAAGATGAAATAGCTACAGTATTACATTCAATTCTTAAAGGAATGGAATACCTTCATT
TTATGAGAAAAATACACTGAGACATCAAGGCAGGAAATATTTTGCTAAATACAGAGGGACATGCAAAACTCACAGATTTT
GGTGTAGCAGGTCAACTTACAGATACCATGGCCAAGCGTAATACAGTAATAGGAACACCATTTTGAATGGCTCCAGAGGT
GATTCAGGAAATTGGGTACAACTGTGTGGCAGACACCTGGTCTCTGGGAATAACTGCTATAGAAATGGCTGAAGGAAAGC
CACCATATGCTGATATCCATCCCATGAGGGCAATCTTCATGATTCCTACAAACCCTCCCCCACATTCCGCAAACCAGAGC
TGTGGTCAGATAACTTTACAGACTTCATGAAGCAGTGTCTTGTAAAGAGCCCTGAGCAGAGGGCCACAGCCACTCAGCTC
CTGAAGCACCCGTTTGTCAGGAATGCTAAAGGAGTGTCAATGTTGTGGGACTTAATTAACGAAGCCATGGATGTGAAACT
GAAACGCCAGGAATCCCAGCAGCGGGAAGTGGACCAAGATGATGAAGATAACTCAGAGGAGGATGAAATGGATTCTGGCA
TGATGGTTCGCGCGGCAGGCGACGAGATGGGCACTGTGTGTGTGGCCAGCACCATGAGTGATGGAGCCAGTACCATGATT
GAGCATGAAGACACCTTGCCCTCACAGCTGGGCACCATGGTGACCAATGCAGAGGATGAGGAAGAGGAAGGGACTATGAA
AATAAGGGATGAGACTATGCAGCCTGTAAAACCATCTTTCCTTGAATACTTTGAACAAAAAGAAAAGGAAAACTAGGTCA
ACAGCTTTGGCAAGAGTGTACCTGCTCCGCTGAAAAATTCTTCCGATTGGAAAGTACCACTGGATGGAGACTATGAGTTT
CTTAAGAGTTGGACAGTGGAGGACCTTCAGAAGAGGCTCTTGGCCCTGGACCCCATGATGGAGCTGGAGATTGAAGAGAT
CCAACGGAAGTACCAGTCCAAGCGGCAGCCAATCCTGGATGCCATCGAGGCTAAGAAGAGGCGGCAGCAAAACTTC

Alignment

ORF - retro_ocun_1122 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.58 %
• Parental protein coverage: 98.36 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPRRQLKKLDEDSLTKQPEEVFDVLEKLGEGSYGSVYKAIHKETGQIVAIKQVPVESDLQEIIKEISIMQ
          P...QLK.LDEDSLTKQPEEV.DVLEKLGE.SYGSVYKAIHKETGQIVAIKQVPVESDLQEIIKEISIMQ
Retrocopy PGAWQLKMLDEDSLTKQPEEVSDVLEKLGERSYGSVYKAIHKETGQIVAIKQVPVESDLQEIIKEISIMQ

Parental  QCDSPHVVKYYGSYFKNTDLWIVMEYCGAGSVSDIIRLRNKTLTEDEIATVLQSTLKGLEYLHFMRKIHR
          QCDSPHVVKYYGSYFKNTDLWIVMEYCGAGSVSDIIRL.NKTLTEDEIATVL.S.LKG.EYLHFMRKIH.
Retrocopy QCDSPHVVKYYGSYFKNTDLWIVMEYCGAGSVSDIIRLQNKTLTEDEIATVLHSILKGMEYLHFMRKIH*

Parental  DIKAGNILLNTEGHAKLADFGVAGQLTDTMAKRNTVIGTPFWMAPEVIQEIGYNCVADIWSLGITAIEMA
          DIKAGNILLNTEGHAKL.DFGVAGQLTDTMAKRNTVIGTPF.MAPEVIQEIGYNCVAD.WSLGITAIEMA
Retrocopy DIKAGNILLNTEGHAKLTDFGVAGQLTDTMAKRNTVIGTPF*MAPEVIQEIGYNCVADTWSLGITAIEMA

Parental  EGKPPYADIHPMRAIFMIPTNPPP-TFRKPELWSDNFTDFVKQCLVKSPEQRATATQLLQHPFVRNAKGV
          EGKPPYADIHPMRAIFMIPTNPPP.TFRKPELWSDNFTDF.KQCLVKSPEQRATATQLL.HPFVRNAKGV
Retrocopy EGKPPYADIHPMRAIFMIPTNPPP<TFRKPELWSDNFTDFMKQCLVKSPEQRATATQLLKHPFVRNAKGV

Parental  SMLRDLINEAMDVKLKRQESQQREVDQDDEDNSEEDEMDSGTMVRAAGDEMGTVRVASTMSDGASTMIEH
          SML.DLINEAMDVKLKRQESQQREVDQDDEDNSEEDEMDSG.MVRAAGDEMGTV.VASTMSDGASTMIEH
Retrocopy SMLWDLINEAMDVKLKRQESQQREVDQDDEDNSEEDEMDSGMMVRAAGDEMGTVCVASTMSDGASTMIEH

Parental  EDTLPSQLGTMVINAEDEEEEGTMKRRDETMQPVKPSFLEYFEQKEKENQVNSFGKSVPAPLKNSSDWKV
          EDTLPSQLGTMV.NAEDEEEEGTMK.RDETMQPVKPSFLEYFEQKEKEN.VNSFGKSVPAPLKNSSDWKV
Retrocopy EDTLPSQLGTMVTNAEDEEEEGTMKIRDETMQPVKPSFLEYFEQKEKEN*VNSFGKSVPAPLKNSSDWKV

Parental  PLDGDYEFLKSWTVEDLQKRLLALDPMMEQEIEEIRQKYQSKRQPILDAIEAKKRRQQNF
          PLDGDYEFLKSWTVEDLQKRLLALDPMME.EIEEI..KYQSKRQPILDAIEAKKRRQQNF
Retrocopy PLDGDYEFLKSWTVEDLQKRLLALDPMMELEIEEIQRKYQSKRQPILDAIEAKKRRQQNF

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	0.06 RPM	7.56 RPM
SRP017611_kidney	0.30 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_1122 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1122 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1122 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,