RetrogeneDB ID: retro_rnor_1560

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:195854234..195855287(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Foxk2
• Ensembl ID: ENSRNOG00000036663
• Aliases: None
• Description: forkhead box protein K2 [Source:RefSeq peptide;Acc:NP_001100545]

Sequence

>retro_rnor_1560
CTCATCAGCCACCTTCCCTCCCCCACGGGAACTATCAGTGCTGCAAACTCCTGCCCATCCAGCCCACAGGGAGCAGGATC
TTCAGGGTACAAAATGGGCCATGTGATACCATCTGACCTCAATTTAATGGCTAACAATTCACAGCCAGAAAATGAAAAGG
AAGCTTCAGGTGGAGACAGCCCAAAGGATGACTCAAAACCACCTTACTCCTATGCACAGTTGATAGTACAAGCAATTACA
ATGGCTCCTGATAAACAACTTACCCTAAATGGGATTTACACACACATCACTAAAAACTATCCATACTACAGGACTGAGGA
CAAGGGCTGGCAGAATTCAACTCACCACAATCTCTCTCTGAACCGTTATTTCATCAAAGTGCCATGTTCTCAGGAAGAAC
CAGGCAAAGGCTCCTTCTGGAGGATAGATCCTGCCTCCGAGAGCAAGCAGGTAGAGCAGGCTTTTAGGAAAAGAGGGCCT
AGGGGTGTGCCTTGCTTTAGAACCCCCCTGGGACCGCTCTCCTCTAGGAGTGTCCCAGCTTCTCCCAACCATGCTGGAGT
GCTGTCTACTCACTCCAGTGGCGCCCAGACCCCCAAGAGCCTGTCGAGGGAAGGCTCCCCAGCCCCCTTGGAGCCTGAGC
CTGGTGCCTCACAGCCCAAACTTGCTGTCATCCAGGAGGAAAGGTTTGCCCAGAGTGCACCAGGGTCACCTCTCTCTAGT
CAGCCCATTTTAATTACTGTCCAGCGGCAGCTACCCCCGGCCATTAAGTCTGTCACCTATACTGTTGCAACCCCAGTGAC
CACACCCACTTCTCAGTCACTGGTCGTGCAGACGGTACATGTTGTCCATCAGATACCAGCAGTGGCAGTCACCAGCGTGG
CTGTACTGGCCCCAGCAAACACGTACACAGTTGCTGGACAAGCTGTGGTCACTGAGGCTGTGGTGCTGGTTCCTCCTAAG
ACTGAACCACAAGAGAATGGCAACCACAGAGAAGTCAGAGTGAAAGTAGAACCTGTCCCTGCAATTAGCCCAGCCACATT
AGGCGCTGCTAGT

Alignment

ORF - retro_rnor_1560 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 87.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LISPLPSPTGTISAANSCPSSPRGAGSSGYKMGRVIPSDLNLMADNSQPENEKEASGGDSPKDDSKPPYS
          LIS.LPSPTGTISAANSCPSSP.GAGSSGYKMG.VIPSDLNLMA.NSQPENEKEASGGDSPKDDSKPPYS
Retrocopy LISHLPSPTGTISAANSCPSSPQGAGSSGYKMGHVIPSDLNLMANNSQPENEKEASGGDSPKDDSKPPYS

Parental  YAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTADKGWQNSIRHNLSLNRYFIKVPRSQEEPGKGSFW
          YAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRT.DKGWQNS..HNLSLNRYFIKVP.SQEEPGKGSFW
Retrocopy YAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTEDKGWQNSTHHNLSLNRYFIKVPCSQEEPGKGSFW

Parental  RIDPASESKLVEQAFRKRRPRGVPCFRTPLGPLSSRSAPASPNHAGVLSAHSSGAQTPESLSREGSPAPL
          RIDPASESK.VEQAFRKR.PRGVPCFRTPLGPLSSRS.PASPNHAGVLS.HSSGAQTP.SLSREGSPAPL
Retrocopy RIDPASESKQVEQAFRKRGPRGVPCFRTPLGPLSSRSVPASPNHAGVLSTHSSGAQTPKSLSREGSPAPL

Parental  EPEPGASQPKLAVIQEARFAQSAPGSPLSSQPVLITVQRQLPPAIKPVTYTVATPVTTPTSQPPVVQTVH
          EPEPGASQPKLAVIQE.RFAQSAPGSPLSSQP.LITVQRQLPPAIK.VTYTVATPVTTPTSQ..VVQTVH
Retrocopy EPEPGASQPKLAVIQEERFAQSAPGSPLSSQPILITVQRQLPPAIKSVTYTVATPVTTPTSQSLVVQTVH

Parental  VVHQIPAVAVTSVAGLAPANTYTVAGQAVVTQAAVLA-PKTEPQENGDHREVRAVASPLHMLATHASASA
          VVHQIPAVAVTSVA.LAPANTYTVAGQAVVT.A.VL..PKTEPQENG.HREVR....P...........A
Retrocopy VVHQIPAVAVTSVAVLAPANTYTVAGQAVVTEAVVLVPPKTEPQENGNHREVRVKVEPVPAISPATLGAA

Parental  S
          S
Retrocopy S

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	0.07 RPM	74.70 RPM
SRP017611_kidney	0.07 RPM	40.82 RPM
SRP017611_liver	0.07 RPM	16.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1560 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1560 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1560 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001235	1 retrocopy	retro_amel_1919,
Rattus norvegicus	ENSRNOG00000036663	1 retrocopy	retro_rnor_1560 ,