RetrogeneDB ID: retro_rnor_1274

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:59052967..59054224(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000017603
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Uhmk1
• Ensembl ID: ENSRNOG00000002941
• Aliases: Uhmk1, KIS, Kist
• Description: Serine/threonine-protein kinase Kist [Source:UniProtKB/Swiss-Prot;Acc:Q63285]

Sequence

>retro_rnor_1274
ATGGCCGGGTCCTGCTGCGCGTGGGGCGCCGAGCCGCCGCGCTTCCTGGAGGCCTTCGGGCGGCTGTGGCAGGTACAGAG
CCGCCTAGGCAGCGGCTCCTCGGCCTCGGTGTACCGGGTGCGCTGCTGCGGCACTCCAGGCTCGCCCCCCGGCGCCCTCA
AGCAGTTCCTGCCTCCGGGAACCACCGGGGCTGCCGCCTCGGCTGCGGAGTATGGTTTCCGAAAAGAGAGGGCAGCGCTG
GAGCAGTTGCAGGGTCACAGGAACATCGTGACTTTATACGGAGTCTTTACCATACACTTCTCTCCAAATGTGCCATCACG
CTGTCTGTTGCTTGAACTCCTGGATGTCAGCGTTTCGGAATTGCTTGTATATTCCAGTCACCAGGGTTGCTCCATGTGGA
TGATACAGCACTGTGCCAGAGATGTTCTGGAGGCCCTTGCTTTTCTTCACCATGAGGGCTATGTCCATGCAGACCTCAAA
CCACGAAACATCCTGTGGAGTGCGGAGAACGAGTGCTTTAAGCTTATTGACTTTGGACTCAGCTTCAAAGAAGGCAATCA
GGACGTGAAGTATATTCAGACAGACGGGTATCGAGCTCCTGAAGCAGAACTGCAGAATTGCTTGGCCCAGGCCGGCCTGC
AGAGTGATACAGAGTGTACCTCAGCTGTTGATCTCTGGAGCCTTGGAATCATTTTACTGGAAATGTTCTCAGGAATGAAA
CTGAAACATACAGTCAGATCTCAGGAGTGGAAGGCAAACAGTTCTGCTATTATTGATCATATATTTGCCAGTAAAGCAGT
GGTGAATGCCGCAATTCCAGCCTATCACCTCAGAGACCTTATCAAAAGCATGCTTCATGACGACCCAAGCAGAAGGATCC
CTGCTGAGATGGCCTTGTGCAGCCCATTCTTTAGCATTCCTTTTGCCCCTCATATTGAAGATCTGGTGATGCTTCCAACT
CCAGTGCTCAGACTCCTCAATGTGCTGGATGATGACTATCTTGAAAATGAAGATGAATATGAAGATGTTGTAGAAGATGT
AAAAGAAGAGTGTCAGAAATATGGACCAGTGGTTTCTCTGCTTGTTCCAAAGGAAAATCCTGGCAGAGGACAAGTCTTTG
TTGAGTACGCAAACGCTGGAGATTCCAAAGCTGCTCAGAAATTGCTGACTGGGAGGATGTTTGATGGGAAGTTTGTTGTG
GCTACATTCTACCCGCTGAGTGCCTACAAGAGGGGATATCTTTATCAAACCTTGCTT

Alignment

ORF - retro_rnor_1274 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGSGCAWGAE-PRFLEAFGRLWQVQSRLGSGSSASVYRVRCCGTPGSPPGALKQFLPPGTTGAAASAAE
          MAGS.CAWGAE.PRFLEAFGRLWQVQSRLGSGSSASVYRVRCCGTPGSPPGALKQFLPPGTTGAAASAAE
Retrocopy MAGSCCAWGAEPPRFLEAFGRLWQVQSRLGSGSSASVYRVRCCGTPGSPPGALKQFLPPGTTGAAASAAE

Parental  YGFRKERAALEQLQGHRNIVTLYGVFTIHFSPNVPSRCLLLELLDVSVSELLVYSSHQGCSMWMIQHCAR
          YGFRKERAALEQLQGHRNIVTLYGVFTIHFSPNVPSRCLLLELLDVSVSELLVYSSHQGCSMWMIQHCAR
Retrocopy YGFRKERAALEQLQGHRNIVTLYGVFTIHFSPNVPSRCLLLELLDVSVSELLVYSSHQGCSMWMIQHCAR

Parental  DVLEALAFLHHEGYVHADLKPRNILWSAENECFKLIDFGLSFKEGNQDVKYIQTDGYRAPEAELQNCLAQ
          DVLEALAFLHHEGYVHADLKPRNILWSAENECFKLIDFGLSFKEGNQDVKYIQTDGYRAPEAELQNCLAQ
Retrocopy DVLEALAFLHHEGYVHADLKPRNILWSAENECFKLIDFGLSFKEGNQDVKYIQTDGYRAPEAELQNCLAQ

Parental  AGLQSDTECTSAVDLWSLGIILLEMFSGMKLKHTVRSQEWKANSSAIIDHIFASKAVVNAAIPAYHLRDL
          AGLQSDTECTSAVDLWSLGIILLEMFSGMKLKHTVRSQEWKANSSAIIDHIFASKAVVNAAIPAYHLRDL
Retrocopy AGLQSDTECTSAVDLWSLGIILLEMFSGMKLKHTVRSQEWKANSSAIIDHIFASKAVVNAAIPAYHLRDL

Parental  IKSMLHDDPSRRIPAEMALCSPFFSIPFAPHIEDLVMLPTPVLRLLNVLDDDYLENEDEYEDVVEDVKEE
          IKSMLHDDPSRRIPAEMALCSPFFSIPFAPHIEDLVMLPTPVLRLLNVLDDDYLENEDEYEDVVEDVKEE
Retrocopy IKSMLHDDPSRRIPAEMALCSPFFSIPFAPHIEDLVMLPTPVLRLLNVLDDDYLENEDEYEDVVEDVKEE

Parental  CQKYGPVVSLLVPKENPGRGQVFVEYANAGDSKAAQKLLTGRMFDGKFVVATFYPLSAYKRGYLYQTLL
          CQKYGPVVSLLVPKENPGRGQVFVEYANAGDSKAAQKLLTGRMFDGKFVVATFYPLSAYKRGYLYQTLL
Retrocopy CQKYGPVVSLLVPKENPGRGQVFVEYANAGDSKAAQKLLTGRMFDGKFVVATFYPLSAYKRGYLYQTLL

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	0.93 RPM	49.68 RPM
SRP017611_kidney	0.42 RPM	31.26 RPM
SRP017611_liver	0.13 RPM	11.36 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1274 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1274 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1274 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000001048	1 retrocopy	retro_mdom_103,
Oryctolagus cuniculus	ENSOCUG00000012411	3 retrocopies	retro_ocun_1245, retro_ocun_1535, retro_ocun_1547,
Rattus norvegicus	ENSRNOG00000002941	1 retrocopy	retro_rnor_1274 ,