RetrogeneDB ID: retro_mmus_2961

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:104821203..104822253(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000086229
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Twf1
• Ensembl ID: ENSMUSG00000022451
• Aliases: Twf1, A6, Ptk9, twinfilin
• Description: twinfilin, actin-binding protein, homolog 1 (Drosophila) [Source:MGI Symbol;Acc:MGI:1100520]

Sequence

>retro_mmus_2961
ATGTCCCACCAGACCAGCATCCAAACAAGCGAAGATGTCAAAGAGATCTTTGCCCGAGCCAGAAACGGGAAATACAGACT
TCTGAAAATATCTATCGAAAATGAGCAACTGGTGGTTGGGTCCTGTAGTCCACTTTCAGATTCCTGGGAACAGGATTACG
ACTCCTTTGTCTTGCCTCTGCTGGAGGACAAGCAGCCGTGCTATGTATTATTCAGGTTAGACTCTCAGAATGCCCAGGGA
TATGAATGGATATTCATTGCGTGGTCTCCAGATCATTCTCATGTACTTCAGAAAATGCTGTATGTAGTAACAAGAGCAAC
TCTGAAGAAAGAATTTGGAGGTGGCCACATTAAAGATGAAGTGTTTGGAACAGTAAAGGAGGACATATCATTACATGGAT
ATAAAAAGTATTTGCTGTCCCAGTCTTCCCCTGCCCCGCTGACCACTCCTGAGGAAGAATTACGGCAGATTAAAATCAAT
GAGGTCCAAACTGATGTGAGTGTGGACACAAAGCACCAGACACTACACGGCGTAGCATTTCCTATTTCTCGAGATGCCTT
CCAGGCTTTGGAGAAGCTGAGTAAGAAGCAGCTCAACTATGTGCAGTTGGAAATAGATATAAAAAATGAAACAATAACTT
TGGCCAACACAGAAAATACAGAACTAAGAGATTTGCCAAAGAGGATTCCCAAGGATTCAGCGCGTTACCATTTCTTTCTG
TATAAGCATTCCCACGAAGGAGACTACTTAGAGTCCGTAGTTTTTATTTATTTGATGCCTGGATACACGTGCAGCATAAG
AGAGCGGATGCTGTATTCCAGCTGCAAGAGCCCTCTGCTCGAGATTGTAGAGCGACAGCTACAGATGGATGTGATCAGAA
AGATTGAGATAGACAATGGTGATGAGCTGACTGCGGATTTCCTGTACGATGAAGTCCACCCCAAGCAGCATGCACATAAG
CAGAGTTTTGCTAAACCGAAAGGTCCTGCGGGAAAGAGGGGGATCCGAAGATTGATTAGGGGCCCAGCGGAAGCAGAAGC
CACTACTGAC

Alignment

ORF - retro_mmus_2961 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.57 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSHQTGIQASEDVKEIFARARNGKYRLLKISIENEQLVVGSCSPPSDSWEQDYDSFVLPLLEDKQPCYVL
          MSHQT.IQ.SEDVKEIFARARNGKYRLLKISIENEQLVVGSCSP.SDSWEQDYDSFVLPLLEDKQPCYVL
Retrocopy MSHQTSIQTSEDVKEIFARARNGKYRLLKISIENEQLVVGSCSPLSDSWEQDYDSFVLPLLEDKQPCYVL

Parental  FRLDSQNAQGYEWIFIAWSPDHSHVRQKMLYAATRATLKKEFGGGHIKDEVFGTVKEDVSLHGYKKYLLS
          FRLDSQNAQGYEWIFIAWSPDHSHV.QKMLY..TRATLKKEFGGGHIKDEVFGTVKED.SLHGYKKYLLS
Retrocopy FRLDSQNAQGYEWIFIAWSPDHSHVLQKMLYVVTRATLKKEFGGGHIKDEVFGTVKEDISLHGYKKYLLS

Parental  QSSPAPLTAAEEELRQIKINEVQTDVSVDTKHQTLQGVAFPISRDAFQALEKLSKKQLNYVQLEIDIKNE
          QSSPAPLT..EEELRQIKINEVQTDVSVDTKHQTL.GVAFPISRDAFQALEKLSKKQLNYVQLEIDIKNE
Retrocopy QSSPAPLTTPEEELRQIKINEVQTDVSVDTKHQTLHGVAFPISRDAFQALEKLSKKQLNYVQLEIDIKNE

Parental  TIILANTENTELRDLPKRIPKDSARYHFFLYKHSHEGDYLESVVFIYSMPGYTCSIRERMLYSSCKSPLL
          TI.LANTENTELRDLPKRIPKDSARYHFFLYKHSHEGDYLESVVFIY.MPGYTCSIRERMLYSSCKSPLL
Retrocopy TITLANTENTELRDLPKRIPKDSARYHFFLYKHSHEGDYLESVVFIYLMPGYTCSIRERMLYSSCKSPLL

Parental  EIVERQLQMDVIRKIEIDNGDELTADFLYDEVHPKQHAHKQSFAKPKGPAGKRGIRRLIRGPAEAEATTD
          EIVERQLQMDVIRKIEIDNGDELTADFLYDEVHPKQHAHKQSFAKPKGPAGKRGIRRLIRGPAEAEATTD
Retrocopy EIVERQLQMDVIRKIEIDNGDELTADFLYDEVHPKQHAHKQSFAKPKGPAGKRGIRRLIRGPAEAEATTD

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
SRP007412_brain	0.07 RPM	34.44 RPM
SRP007412_cerebellum	0.00 RPM	30.61 RPM
SRP007412_heart	0.03 RPM	14.69 RPM
SRP007412_kidney	0.04 RPM	54.92 RPM
SRP007412_liver	0.05 RPM	45.30 RPM
SRP007412_testis	1.14 RPM	14.87 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2961 was not detected

EST

No EST(s) were mapped for retro_mmus_2961 retrocopy.

TSS

No TSS is located nearby retro_mmus_2961 retrocopy 5' end.

Lab

retro_mmus_2961 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2961 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017332	1 retrocopy	retro_amel_1224,
Choloepus hoffmanni	ENSCHOG00000008386	5 retrocopies	retro_chof_1525, retro_chof_2013, retro_chof_2569, retro_chof_391, retro_chof_509,
Homo sapiens	ENSG00000151239	2 retrocopies	retro_hsap_1819, retro_hsap_4916,
Monodelphis domestica	ENSMODG00000018535	1 retrocopy	retro_mdom_167,
Mustela putorius furo	ENSMPUG00000000364	1 retrocopy	retro_mputfur_1629,
Mus musculus	ENSMUSG00000022451	1 retrocopy	retro_mmus_2961 ,
Nomascus leucogenys	ENSNLEG00000017931	1 retrocopy	retro_nleu_2877,
Otolemur garnettii	ENSOGAG00000007525	1 retrocopy	retro_ogar_1058,
Pan troglodytes	ENSPTRG00000004846	1 retrocopy	retro_ptro_3279,
Rattus norvegicus	ENSRNOG00000022507	1 retrocopy	retro_rnor_2176,