RetrogeneDB ID: retro_rnor_2045

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:30437812..30439819(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000050175
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Vil1
• Ensembl ID: ENSRNOG00000015408
• Aliases: Vil1, Vil
• Description: villin-1 [Source:RefSeq peptide;Acc:NP_001101694]

Sequence

>retro_rnor_2045
AGAAGTTTCAACAGAGGGGATGTCTTCCTGCTGGACCTTGGGAAGCTTACCATCCAGTGGAATGGGCCTGAGAGTAACTG
CATGGAGAGACTTCGTGGCATGACTTTGGCCAAAGAGATCCGAGACCAGGAGCAGGGTGGACGCACCTACGTAGGCGTGG
TGGATCGGGAGAAGGAAGGGGACTCCCTACAGTTGATGGCAATTATGATCCACATGCTGGGCCCACGCAAGGAACTGAAG
GCTGCAATTTCTGATTCAGTGGTGGAGCCGGCTGCTAAGGCTGCACTCAAGCTGTACCATGTGTCTGATTCAGAAGGAAA
AATAGTTGTTAGAGAAGTTGCTACTTGGCCACTCACACAGGACTTGCTCAGTCATGAGGACTGTTACATCCTGGACCAGG
GAGGCCTGAAGATCTTTGTGTGGAAGGGAAAAAATGCCAATGCCCAGGAGCGGAGTGGAGCCATGAACCAAGCCTTGAAC
TTCATCAAAGCCAAGCAGTACCCACCTAGCATGCAGGTTGAGGTACAGAACAATAGGGCCGAGTCTGCCATTTTCCAGCA
GCTTTTCCAGAAGTGGACAGTGCCCAATCGGACCTCAGGCCTCGGCAAGACCCACACAGTGGGCTCTGTGGCCAAGGTGG
AACCGGTGAAGTTTGATGCTCTGTCCATGCACGTACAGCCTCAAGTGGCTGCCCAGCAGAAAATGGTGGATGACAGGAGT
GGGGAAGTGCAGGTGTGGCGCATCAAGGACTTAGAGCTGGTGCCTGTGGAGTCCAAGTGCTGGGCCATTTCTACGGTGGC
GACTGCTACCTACTACTCTACACCTACCTCATAGGCGAGAAGGAACACTACTTGCTGTATATCTGGCAGGGCAGCCAGGC
CAGCCAGGATGAAATTGCAGCCTCGGTTTACCAAGCTGTCAACCTGGACTAGAGGTACAACGACGAGCCAGTGCAGATCC
GGGTCACAAAGGGCAAGTATCCGCCTCACCTCATGTCTATCTTCAAGGGGCGCATGGTGGTTTATCAGGGAGGCACCTCC
TGAAAGAACAACGTGGAGCACGTGCCCTCTACAAGGCTGTTTCAGGTCCGAGGGAACAGTGCTGATAACACCAAGGCTTT
TGAGGTTACAGCCCGGGCTACCTTCCTCAACTCCAGTGACGTCTTCATACTCAAGACTCCGTCCTGCTGCTATACCTGTG
GTGTGGAAAGGGTTGTAGTGGGGATGAGCGGCAGATGGCCAAGATGGCTGCTGATACCATCTCTCGGACAGAGAAGCAAG
TGGTGGTCGAGGGGCAGGAGCCAGCCAACTTCTGGATGGCTCTGGGTGGGAAGGTGCCCTATGCCAACACCAAGAGGCTG
CAGGAGGAAAACCAAGTCATCACTCCTCGGCTCTTTGAGTGCTCCAACCAGACCGGGCGCTTTCTGGCCACAGAGATTTT
TGACTTCACTCAGGAGGACCTGGAAGAGGAGGATGTGTTCCTATTGGTTGTCTGGGACCAGGTCTTCTGGATAGGGAAAC
GCGCCAATGAGGAAGAAAAGAAGGCTGCAGCTACAACTGCACAGGAATACCTCAAGATCCATCCCGAAACAGAGACCCTG
AGACCCCTATCATTGTGGTGAAGCAGGGGCACGAGCCCCCCACCTTCACAGGCTGGTTCCTGGCTTGGGATCCCTTCAAG
TGGAGTAACACCAAATCTTATGATGACCTCAAGGCCGAGCTGGGAAACTCTGGGGACTGAAGCCAGATTGCTGATGAGGT
TATGAGCCCCAAAGTGGACGTTTTCACTGCCAATACCAGCTTCAGTTCTGGGCCCTTGCCCATCTTTCCCCTGGAGCAGC
TGGTAAACAAGCCTGTGGAGGAGCTCCCTGAGGGTGTGGATCCCACCAGGAAGGAGGAGCACCTGTCCACTGAAGATTTC
ACTAAGGCTTTGGGGATGACTCCAGCTGCCTTCTCTGCCCTGCCTGGATGGAAGCAACAAAACCTCAAGAAAGAAAAAGG
ACTGTTT

Alignment

ORF - retro_rnor_2045 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.88 %
• Parental protein coverage: 81.02 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KSFNRGDVFLLDLGKLIIQWNGPESNRMERLRGMTLAKEIRDQERGGRTYVGVVDGENEGDSPQLMAIMN
          .SFNRGDVFLLDLGKL.IQWNGPESN.MERLRGMTLAKEIRDQE.GGRTYVGVVD.E.EGDS.QLMAIM.
Retrocopy RSFNRGDVFLLDLGKLTIQWNGPESNCMERLRGMTLAKEIRDQEQGGRTYVGVVDREKEGDSLQLMAIMI

Parental  HVLGPRKELKAAISDSVVEPAAKAALKLYHVSDSEGKMVVREVATQPLTQDLLSHEDCYILDQGGLKIFV
          H.LGPRKELKAAISDSVVEPAAKAALKLYHVSDSEGK.VVREVAT.PLTQDLLSHEDCYILDQGGLKIFV
Retrocopy HMLGPRKELKAAISDSVVEPAAKAALKLYHVSDSEGKIVVREVATWPLTQDLLSHEDCYILDQGGLKIFV

Parental  WKGKNANAQERSGAMNQALNFIKAKQYPPSTQVEVQNDGAESAIFQQLFQKWTVPNRTSGLGKTHTVGSV
          WKGKNANAQERSGAMNQALNFIKAKQYPPS.QVEVQN..AESAIFQQLFQKWTVPNRTSGLGKTHTVGSV
Retrocopy WKGKNANAQERSGAMNQALNFIKAKQYPPSMQVEVQNNRAESAIFQQLFQKWTVPNRTSGLGKTHTVGSV

Parental  AKVEQVKFDALSMHVRPQVAAQQKMVDDGSGEVQVWRIEDLELVPVESKW-LGHFYGGDCYLLLYTYLIG
          AKVE.VKFDALSMHV.PQVAAQQKMVDD.SGEVQVWRI.DLELVPVESK..LGHFYGGDCYLLLYTYLIG
Retrocopy AKVEPVKFDALSMHVQPQVAAQQKMVDDRSGEVQVWRIKDLELVPVESKC<LGHFYGGDCYLLLYTYLIG

Parental  EKEHYLLYIWQGSQASQDEIAASAYQAVNLDQKYNDEPVQIRVTMGKEPPHLMSIFKGRMVVYQGGTSRK
          EKEHYLLYIWQGSQASQDEIAAS.YQAVNLD..YNDEPVQIRVT.GK.PPHLMSIFKGRMVVYQGGTS.K
Retrocopy EKEHYLLYIWQGSQASQDEIAASVYQAVNLD*RYNDEPVQIRVTKGKYPPHLMSIFKGRMVVYQGGTS*K

Parental  NNVEPVPSTRLFQVRGTSADNTKAFEVTARATSLNSNDVFILKTPS-C-CYLWCGKGCSGDEREMAKMVA
          NNVE.VPSTRLFQVRG.SADNTKAFEVTARAT.LNS.DVFILKTPS.C..YLWCGKGCSGDER.MAKM.A
Retrocopy NNVEHVPSTRLFQVRGNSADNTKAFEVTARATFLNSSDVFILKTPSCC<LYLWCGKGCSGDERQMAKMAA

Parental  DTISRTEKQVVVEGQEPANFWMALGGKAPYANTKRLQEENQVITPRLFECSNQTGRFLATEIFDFTQDDL
          DTISRTEKQVVVEGQEPANFWMALGGK.PYANTKRLQEENQVITPRLFECSNQTGRFLATEIFDFTQ.DL
Retrocopy DTISRTEKQVVVEGQEPANFWMALGGKVPYANTKRLQEENQVITPRLFECSNQTGRFLATEIFDFTQEDL

Parental  EEDDVFLLDVWDQVFFWIGKHANEEEKKAAATTAQEYLKTHPG-NRDPETPIIVVKQGHEPSTFTGWFLA
          EE.DVFLL.VWDQVF.WIGK.ANEEEKKAAATTAQEYLK.HP..NRDPETPIIVVKQGHEP.TFTGWFLA
Retrocopy EEEDVFLLVVWDQVF-WIGKRANEEEKKAAATTAQEYLKIHPE<NRDPETPIIVVKQGHEPPTFTGWFLA

Parental  WDPFKWSNTKSYDDLKAELGNSGDWSQIADEVMSPKVDVFTANTSFSSGPLPIYPLEQLVNKPVEELPEG
          WDPFKWSNTKSYDDLKAELGNSGD.SQIADEVMSPKVDVFTANTSFSSGPLPI.PLEQLVNKPVEELPEG
Retrocopy WDPFKWSNTKSYDDLKAELGNSGD*SQIADEVMSPKVDVFTANTSFSSGPLPIFPLEQLVNKPVEELPEG

Parental  VDPTRKEEHLSTEDFTKALGMTPAAFSALPRWKQQNLKKEKGLF
          VDPTRKEEHLSTEDFTKALGMTPAAFSALP.WKQQNLKKEKGLF
Retrocopy VDPTRKEEHLSTEDFTKALGMTPAAFSALPGWKQQNLKKEKGLF

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	0.00 RPM	0.29 RPM
SRP017611_kidney	0.00 RPM	126.17 RPM
SRP017611_liver	2.49 RPM	0.54 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2045 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2045 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2045 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
Rattus norvegicus	ENSRNOG00000013668	1 retrocopy	retro_rnor_840,
Rattus norvegicus	ENSRNOG00000015408	1 retrocopy	retro_rnor_2045 ,