RetrogeneDB ID: retro_mmus_1629

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:28075408..28076355(-)
• Located in intron of: ENSMUSG00000062859

Retrocopy information

• Ensembl ID: ENSMUSG00000085521
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tsen34
• Ensembl ID: ENSMUSG00000035585
• Aliases: Tsen34, 0610027F08Rik, Leng5
• Description: tRNA splicing endonuclease 34 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1913328]

Sequence

>retro_mmus_1629
ATGCTGGTGGTGGAGGTCGCAAATGGCCGCTCGCTGGTGTGGGGAGCCGAGGCCGTGCAGGCGCTGCGGGAGCGTCTGGG
AGTCGGAGGACGCTCGGTGGGCGCCCTGCCCCGCGGGCCCCGCCAGAACTCGCGCCTGGGCCTTCCGCTTCTGCTGCTGT
CTGAAGAAGCCCGGCTCCTGGCCGAGATAGGCGCGGTGACCCTAGTCAGCGCCCCTCGCCCGGACCCCCGCAACCATGGC
TTGGCCCTAGCATCGTTCAAACGCCAGCAAGAGCAGAGTTTCCAGGATCAGAACACTTTGGCAGCCGAGGCCCGGGAGAC
CCGGCGTCAGGAGCTTCTAGAGAAGATCATAGAGGGCCAGGCACCAAGAAGCAGAAGCTGGAACAGGATTCAGGGGCAGA
TGAAGAAGGCCAAGAAGCCGGTGGAAGTGAGGCTACCCAAGGGAGTGAGAACAGTGATGATGGCCAGCCTTCTGCGGAGC
AGGAGGGAGCAGCCCCATCCCTAGATTCTTTATCTCCACAACCAGGACCTTCAAATGGGGTGACTCCCTTGCCCAGATCA
GCCCTGCTTATCCAGCTGGCCACTGCCAGGCCTCGGCCTGTAAAAGCTAAGCCTCTGGACTGGCGTGTGCAGTCCAAAGA
CTGGCCCCATGCTGGCCGTCCTGCCCACGAGCTGCGCTACAGCATCTACCGAGACCTGTGGGAGAGAGGCTTCTTCCTCA
GCGCAGCAGGGAAGTTTGGTGGTGACTTCCTGGTGTATCCTGGTGATCCACTGCGTTTCCATGCTCACTACATTGCTCAG
TGCTGGTCTGCTGAGGACCCCATCCCACTTCAGGACCTGCTCTCTGCAGGCCGCCTGGGAACCAGTGTCAGGAAGACCCT
GCTGCTCTGCTCCCCTCAGCCTGATGGGAAGGTGGTCTACACATCCCTGCAGTGGGCCAGCCTGCAG

Alignment

ORF - retro_mmus_1629 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.16 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLVVEVANGRSLVWGAEAVQALRERLGVGGRTVGALPRGPRQNSRLGLPLLLLPEEARLLAEIGAVTLVS
          MLVVEVANGRSLVWGAEAVQALRERLGVGGR.VGALPRGPRQNSRLGLPLLLL.EEARLLAEIGAVTLVS
Retrocopy MLVVEVANGRSLVWGAEAVQALRERLGVGGRSVGALPRGPRQNSRLGLPLLLLSEEARLLAEIGAVTLVS

Parental  APRPDPRNHGLALASFKRQQEQSFQDQNTLAAEARETRRQELLEKIVEGQA-AKKQKLEQDSGADEGGQE
          APRPDPRNHGLALASFKRQQEQSFQDQNTLAAEARETRRQELLEKI.EGQA..KKQKLEQDSGADE.GQE
Retrocopy APRPDPRNHGLALASFKRQQEQSFQDQNTLAAEARETRRQELLEKIIEGQA<TKKQKLEQDSGADEEGQE

Parental  AGGSEATQGSETSDDGQPSAEQEGAAPSLDSSSPQPGPSNGVTPLPRSALLIQLATARPRPVKAKPLDWR
          AGGSEATQGSE.SDDGQPSAEQEGAAPSLDS.SPQPGPSNGVTPLPRSALLIQLATARPRPVKAKPLDWR
Retrocopy AGGSEATQGSENSDDGQPSAEQEGAAPSLDSLSPQPGPSNGVTPLPRSALLIQLATARPRPVKAKPLDWR

Parental  VQSKDWPHAGRPAHELRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRFHAHYIAQCWSAEDPIPLQD
          VQSKDWPHAGRPAHELRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRFHAHYIAQCWSAEDPIPLQD
Retrocopy VQSKDWPHAGRPAHELRYSIYRDLWERGFFLSAAGKFGGDFLVYPGDPLRFHAHYIAQCWSAEDPIPLQD

Parental  LVSAGRLGTSVRKTLLLCSPQPDGKVVYTSLQWASLQ
          L.SAGRLGTSVRKTLLLCSPQPDGKVVYTSLQWASLQ
Retrocopy LLSAGRLGTSVRKTLLLCSPQPDGKVVYTSLQWASLQ

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	0.02 RPM	22.57 RPM
SRP007412_cerebellum	0.00 RPM	27.75 RPM
SRP007412_heart	0.09 RPM	30.20 RPM
SRP007412_kidney	0.06 RPM	20.81 RPM
SRP007412_liver	0.03 RPM	12.81 RPM
SRP007412_testis	5.49 RPM	3.93 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1629 was not detected

EST

No EST(s) were mapped for retro_mmus_1629 retrocopy.

TSS

No TSS is located nearby retro_mmus_1629 retrocopy 5' end.

Lab

retro_mmus_1629 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1629 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000002409	1 retrocopy	retro_mmur_1488,
Mus musculus	ENSMUSG00000035585	1 retrocopy	retro_mmus_1629 ,
Rattus norvegicus	ENSRNOG00000011468	1 retrocopy	retro_rnor_1385,