RetrogeneDB ID: retro_rnor_1740

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 20:40271202..40272220(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000047889
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Twf2
• Ensembl ID: ENSRNOG00000048915
• Aliases: None
• Description: twinfilin, actin-binding protein, homolog 2 (Drosophila) [Source:MGI Symbol;Acc:MGI:1346078]

Sequence

>retro_rnor_1740
ATGGTGCACCAGACCGGCATACACGCCACTTGAAGAACTAAAGGACTTCTTTGCCAGGGCCCAGACTGGTTCCATCCGAC
TTATTAGAGTCATCATTGAGGACGAGCAGCTTGTGCTGGGTGCCTCGCAGGAGCCAGTGGGACGTTGGGACCAGGACTAC
GACAGGGACGTGCTGCCACTGCTAGATGCCCAAGAGCCCTGCTACCTCCTCTTCCAACTTGATTCGCAAAATGCTCAGGG
TTTCGAGTGGCTTTTCCTGGCCTGGTCACCTGACAATTCGCCTGTGCAGCTGAAGAAGCTGTATGCAGCCACACGAGCCA
CATTTAAGGAGTTTGGAGGCGGCCACATCAAGGATGAGCGCTTCGGGATAGTAAAGGATGACCTCTCCTTGCCTGGCTTG
AGAAGCCCCTGTCATCCTGTGCTGCACATGCCCCACTGACTTCGGCTGAGCGAGAGATCCAGCAGATCCGAATCAATGAG
GTGAAGACTGACATCAGCGTAGAAAGTAAGCACCTGACCCTGCAGGGCCTGGCTTTGCCCCTGCAGCCTGAGGTCCAGCG
GGCAGTTCAGCAACTCAAGCAGAAGACAGGCAACTATATCCAGCTGAAGCTGGACCTGGAGCGGGAGACCATCGAGCTGG
TACACGCAGAACCCACAAATGTGGCCCAGCTGCCTTCACGGGTTCCCCAAGATGCTGCCCACTACCACTTCTTCCTGGAC
AAGCATACGCATGAGGGTGACTCCCTTGAATCTGTGGTCTTCGTCTACTCCATGCCGGGGTACAAGTGCAGCATTAAGGA
GAGCATGCTCTACTCCAGCAGCGAGAGCCGCCTCCTTGACTCTGTAGAGCAAGACTTCCAGCTGGAGGTAGCTAAGAAGA
TGGAGACCAGCGATGGGGCGGAGCTGACTGCTGAGTTCCTCTATGATGAGGTGCATCCCAAGCAGCACGCCTTCAAGCAG
GCGTTCGCCAAGCCCAAAGGCCCCGGGGGGCAAGCGGGGCCACAGGCGCCTCATCAGG

Alignment

ORF - retro_rnor_1740 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.76 %
• Parental protein coverage: 97.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAHQTGIHAT-EELKEFFAKARAGSIRLIKVIIEDEQLVLGASQEPVGRWDQDYDRAVLPLLDAQEPCYL
          M.HQTGIHAT.EELK.FFA.A..GSIRLI.VIIEDEQLVLGASQEPVGRWDQDYDR.VLPLLDAQEPCYL
Retrocopy MVHQTGIHAT>EELKDFFARAQTGSIRLIRVIIEDEQLVLGASQEPVGRWDQDYDRDVLPLLDAQEPCYL

Parental  LFRLDSQNAQGFEWLFLAWSPDNSPVRLKMLYAATRATVKKEFGGGHIKDELFGTVKDDLSLAGY-QKHL
          LF.LDSQNAQGFEWLFLAWSPDNSPV.LK.LYAATRAT.K.EFGGGHIKDE.FG.VKDDLSL.G...K.L
Retrocopy LFQLDSQNAQGFEWLFLAWSPDNSPVQLKKLYAATRATFK-EFGGGHIKDERFGIVKDDLSLPGL<EKPL

Parental  SSCAAPAPLTSAERELQQIRINEVKTEISVESKHQTLQGLAFPLQPEAQRALQQLKQKTVNYIQLKLDLE
          SSCAA.APLTSAERE.QQIRINEVKT.ISVESKH.TLQGLA.PLQPE.QRA.QQLKQKT.NYIQLKLDLE
Retrocopy SSCAAHAPLTSAEREIQQIRINEVKTDISVESKHLTLQGLALPLQPEVQRAVQQLKQKTGNYIQLKLDLE

Parental  RETIELVHTEPTNVAQLPSRVPRDAARYHFFLYKHTHEGDSLESVVFIYSMPGYKCSIKERMLYSSCKSR
          RETIELVH.EPTNVAQLPSRVP.DAA.YHFFL.KHTHEGDSLESVVF.YSMPGYKCSIKE.MLYSS..SR
Retrocopy RETIELVHAEPTNVAQLPSRVPQDAAHYHFFLDKHTHEGDSLESVVFVYSMPGYKCSIKESMLYSSSESR

Parental  LLDSVEQDFQLEIAKKIEIGDGAELTAEFLYDEVHPKQHAFKQAFAKPKGPGG-KRGHKRLIR
          LLDSVEQDFQLE.AKK.E..DGAELTAEFLYDEVHPKQHAFKQAFAKPKGPGG.KRGH.RLIR
Retrocopy LLDSVEQDFQLEVAKKMETSDGAELTAEFLYDEVHPKQHAFKQAFAKPKGPGG>KRGHRRLIR

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	23.87 RPM
SRP017611_kidney	0.00 RPM	4.61 RPM
SRP017611_liver	0.00 RPM	1.41 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1740 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1740 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1740 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
Rattus norvegicus	ENSRNOG00000022507	1 retrocopy	retro_rnor_2176,
Rattus norvegicus	ENSRNOG00000048915	2 retrocopies	retro_rnor_1740 , retro_rnor_1908,