RetrogeneDB ID: retro_rnor_592

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:91021001..91022123(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000037415
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Kpna4
• Ensembl ID: ENSRNOG00000010768
• Aliases: Kpna4, importin
• Description: importin subunit alpha-4 [Source:RefSeq peptide;Acc:NP_001014793]

Sequence

>retro_rnor_592
GAACAGACGCAAGCAGTGGTTCAGTCCAGTGCTTTGCCACTTTTCCTGAGGCTTCTGCATTCACCCCATCAGAATGTCTA
TGAACAGGCAGTGTGGGTATTGGGAAACCTCATAGGTGATGGACCTCAGTGTAGACATTATGTGATATGCCTTGGAGTTG
TAAAACCTCTGCTTTCATTCATAAGTCCATCTATTCCTATAACATTCTTAAGAAATGTTACCTGGGTCATGGTCAACTTA
TGTCTCCACAAGGACCCACCACCACCAATGGGGACAATTCAGGAGATTCTTCTAGCTCTTTGTGTATTAATTCATCACAC
AGATGTAAATATACTGGTAGATACGGTCTGGGCCCTATCTTACCTTACGGATGCTGGCAATGAGCAGATGCAGATGGTAA
TAGACTCTGGAATAGTTCCTCACTTGGTTCCACTACTCAGCCACCAGGAAGTTAAAGTTCAGACTGCTGCGCTGCGAGCT
GTGGGCAACATTGTCACTGGGACTGATGAGCAAACACAAGTAGTTTTAAACTGTGATGCTCTCTCACACTTCCCAGCACT
CCTCACTCATCCCAAAGAGAAAATTAATAAGGAAGCAGTGTGGTTCCTCTCCAACATCACCGCAGGAAATCAACAGCAGG
TTCAGGCAGTAATTGATGCCAATCTTGTACCAATGATAATACACCTTTTGGATAAGGGAGATTTTGGCACTCAGAAAGAA
GCTGCTTGGGCCATAAGTAACTTAACAATTAGTGGGAGGAAAGACCAAGTCGCCTATCTCATCCAACAAAATGCTATTCC
ACCTCTTTGCAATTTGGTGACTGTAAAAGATGCACAAGTTGTGCAAGTAGTGCTTGATGGACTAAGTAATATATTAAAAA
TGGCTGAAGATCAAGCAGAAACCATAGCCAATCTCATAGAAGAATGTGGTGGACTGGAGAAAATTGAACAACTTCAGAAT
CATGAAAATGAGGACATCTACAAATTGGCCTATGAGATCATTGACCAGTTCTTCTCTTCAGATGATATTGACGAAGATCC
TAGCCTTGTTCCAGAGTCAGTTCAAGGTGGAGCATTTGGTTTCAATTCATCTACTAATGTACCAACAGAAGGGTTCCAGT
TT

Alignment

ORF - retro_rnor_592 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.99 %
• Parental protein coverage: 71.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EQTQAVVQSNAVPLFLRLLHSPHQNVCEQAVWALGNIIGDGPQCRDYVISLGVVKPLLSFISPSIPITFL
          EQTQAVVQS.A.PLFLRLLHSPHQNV.EQAVW.LGN.IGDGPQCR.YVI.LGVVKPLLSFISPSIPITFL
Retrocopy EQTQAVVQSSALPLFLRLLHSPHQNVYEQAVWVLGNLIGDGPQCRHYVICLGVVKPLLSFISPSIPITFL

Parental  RNVTWVMVNLCRHKDPPPPMETIQEILPALCVLIHHTDVNILVDTVWALSYLTDAGNEQIQMVIDSGIVP
          RNVTWVMVNLC.HKDPPPPM.TIQEIL.ALCVLIHHTDVNILVDTVWALSYLTDAGNEQ.QMVIDSGIVP
Retrocopy RNVTWVMVNLCLHKDPPPPMGTIQEILLALCVLIHHTDVNILVDTVWALSYLTDAGNEQMQMVIDSGIVP

Parental  HLVPLLSHQEVKVQTAALRAVGNIVTGTDEQTQVVLNCDALSHFPALLTHPKEKINKEAVWFLSNITAGN
          HLVPLLSHQEVKVQTAALRAVGNIVTGTDEQTQVVLNCDALSHFPALLTHPKEKINKEAVWFLSNITAGN
Retrocopy HLVPLLSHQEVKVQTAALRAVGNIVTGTDEQTQVVLNCDALSHFPALLTHPKEKINKEAVWFLSNITAGN

Parental  QQQVQAVIDANLVPMIIHLLDKGDFGTQKEAAWAISNLTISGRKDQVAYLIQQNVIPPFCNLLTVKDAQV
          QQQVQAVIDANLVPMIIHLLDKGDFGTQKEAAWAISNLTISGRKDQVAYLIQQN.IPP.CNL.TVKDAQV
Retrocopy QQQVQAVIDANLVPMIIHLLDKGDFGTQKEAAWAISNLTISGRKDQVAYLIQQNAIPPLCNLVTVKDAQV

Parental  VQVVLDGLSNILKMAEDQAETIANLIEECGGLEKIEQLQNHENEDIYKLAYEIIDQFFSSDDIDEDPSLV
          VQVVLDGLSNILKMAEDQAETIANLIEECGGLEKIEQLQNHENEDIYKLAYEIIDQFFSSDDIDEDPSLV
Retrocopy VQVVLDGLSNILKMAEDQAETIANLIEECGGLEKIEQLQNHENEDIYKLAYEIIDQFFSSDDIDEDPSLV

Parental  PESVQGGTFGFNSSTNVPTEGFQF
          PESVQGG.FGFNSSTNVPTEGFQF
Retrocopy PESVQGGAFGFNSSTNVPTEGFQF

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	58.31 RPM
SRP017611_kidney	0.07 RPM	77.95 RPM
SRP017611_liver	0.00 RPM	36.38 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_592 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_592 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_592 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008565	2 retrocopies	retro_chof_1082, retro_chof_823,
Echinops telfairi	ENSETEG00000019546	1 retrocopy	retro_etel_1695,
Rattus norvegicus	ENSRNOG00000010768	1 retrocopy	retro_rnor_592 ,
Rattus norvegicus	ENSRNOG00000014945	1 retrocopy	retro_rnor_987,
Rattus norvegicus	ENSRNOG00000015329	1 retrocopy	retro_rnor_42,