RetrogeneDB ID: retro_mmus_3132

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:51879562..51880194(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Tmem189
• Ensembl ID: ENSMUSG00000090213
• Aliases: None
• Description: transmembrane protein 189 [Source:MGI Symbol;Acc:MGI:2142624]

Sequence

>retro_mmus_3132
CACTTGGTCCACCTTCTGTTGCTGGCCAGCTGGGAGCACACACCCCTCGTCATCCTAGGTGTCATTGCAGGGGCTCTTGT
TGCTGACTTCCTGTCCGGCCTGGTACATTGGGGTGCTGATACGTGGGCTCTGTGGATCTGCCCATTGTCGGAAAGGCCTT
CATCCAGCCGTTCCGGGAGCACCACATTGACCCCACAGCCATGACAAGGCACGACTTCATCGAGACCAATGGGAACAACT
GCCTGGTCACACTGCTGCCACTGCTAAACATGGCCTACAAGTTCCGGACCCAGAGCCCAGAGACCCTGGAGGAGCTCTAC
CCTTGGGAATGCTTCGTCTTCTGTCTGACCATCTTTGGCACCTTCACCAACCAGATCCACAAGTGGTCACACACGTACTT
AGGGCTGCCATGCTGGGTCACCGTCCTGTAGGACTGGCACGTGATCCTACAACAGAAACACCATCGCATCCACCACATGG
CGGCCCACAAAACATACTTCTGTATCAACACAGGCTGGCTCAACTACCGCCTAGAGGTTATAGGCTTCTGGCGGCACCTG
GAGGATCTCATCCAAGGCCTGATTGGTGAGAAGCCGAGAGCAGACGACATGAAATGGGCCCAGAAGTTCAAG

Alignment

ORF - retro_mmus_3132 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.57 %
• Parental protein coverage: 77.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NLVHLLLLARWEHTPLVILGVVAGALVADFLSGLVHWGADTW-GSVDLPIVGKAFIRPFREHHIDPTAIT
          .LVHLLLLA.WEHTPLVILGV.AGALVADFLSGLVHWGADTW.GSVDLPIVGKAFI.PFREHHIDPTA.T
Retrocopy HLVHLLLLASWEHTPLVILGVIAGALVADFLSGLVHWGADTW<GSVDLPIVGKAFIQPFREHHIDPTAMT

Parental  RHDFIETNGDNCLVTLLPLLNMAYKFRTQSPETLEQLYPWECFVFCLTIFGTFTNQIHKWSHTYLGLPYW
          RHDFIETNG.NCLVTLLPLLNMAYKFRTQSPETLE.LYPWECFVFCLTIFGTFTNQIHKWSHTYLGLP.W
Retrocopy RHDFIETNGNNCLVTLLPLLNMAYKFRTQSPETLEELYPWECFVFCLTIFGTFTNQIHKWSHTYLGLPCW

Parental  VTVLQDWHVILPRKHHRIHHVAPHETYFCITTGWLNYPLEVIGFWRRLEDLIQGLTGEKPRADDMKWAQK
          VTVL.DWHVIL..KHHRIHH.A.H.TYFCI.TGWLNY.LEVIGFWR.LEDLIQGL.GEKPRADDMKWAQK
Retrocopy VTVL*DWHVILQQKHHRIHHMAAHKTYFCINTGWLNYRLEVIGFWRHLEDLIQGLIGEKPRADDMKWAQK

Parental  IK
          .K
Retrocopy FK

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	0.00 RPM	17.01 RPM
SRP007412_cerebellum	0.00 RPM	17.28 RPM
SRP007412_heart	0.00 RPM	17.93 RPM
SRP007412_kidney	0.02 RPM	85.08 RPM
SRP007412_liver	0.00 RPM	9.15 RPM
SRP007412_testis	0.00 RPM	22.37 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3132 was not detected

EST

No EST(s) were mapped for retro_mmus_3132 retrocopy.

TSS

No TSS is located nearby retro_mmus_3132 retrocopy 5' end.

Lab

retro_mmus_3132 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3132 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000022674	4 retrocopies	retro_mmus_1385, retro_mmus_189, retro_mmus_2048, retro_mmus_2770,
Mus musculus	ENSMUSG00000090213	2 retrocopies	retro_mmus_2219, retro_mmus_3132 ,
Otolemur garnettii	ENSOGAG00000009132	1 retrocopy	retro_ogar_3171,