RetrogeneDB ID: retro_mmus_2219

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:8462227..8462860(-)
• 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_2219
GACTTGGTCCACCTCCTGCTGCTGGCCCGCTGGGAGCACACACCCCTCGTGATCCTGGGTGTCGTTGCAGGGGCTCTCGT
CGCTGACTTCCTGTCCGGCCTGGTACATTGGGGTGCTGATACGTGGGGCCCTGTGGATCTGCCCATTGTTGGGAAGGCCT
TCATCCGGCCGTTCCGGGAGCACCACATTGACCCCACAGCCATCACAAGGCACGACTTCATCGAGACCAATGAGGACAAC
TGCCTGGTCACGCTGCTGCCACTGCTAAACATGGCCTACAAGTTCCGGACCCATAGCTCAGAGACCCTGGAGCAGCTGTA
CCCTTGGGAATGCTTCGTCTTCTGTCTGACCATCTTTGGCACCTTCACCAACCAGATCCACAAGTGGTCACACACATACT
TAGGGCTGCCATGCTGGGTCACTGTCCTGCAGGACTGGCACGTGATCCTACCACGGAAACACCGTTGCATCCACCACGTG
GCGGCCCACGAAACATCCTTCTGTATCACTACAGGCTGGCTCAACTACCGCCCAGAGGTTATAGGCTTCTGGCGGCGCCT
GGAGGATCTCATCCAAGGTCTGACGGGTGAGAAGCCGAGAGCGGACGACATGAAATGGGCCCAGAAGATCAAG

Alignment

ORF - retro_mmus_2219 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.31 %
• Parental protein coverage: 77.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NLVHLLLLARWEHTPLVILGVVAGALVADFLSGLVHWGADTWGSVDLPIVGKAFIRPFREHHIDPTAITR
          .LVHLLLLARWEHTPLVILGVVAGALVADFLSGLVHWGADTWG.VDLPIVGKAFIRPFREHHIDPTAITR
Retrocopy DLVHLLLLARWEHTPLVILGVVAGALVADFLSGLVHWGADTWGPVDLPIVGKAFIRPFREHHIDPTAITR

Parental  HDFIETNGDNCLVTLLPLLNMAYKFRTQSPETLEQLYPWECFVFCLTIFGTFTNQIHKWSHTYLGLPYWV
          HDFIETN.DNCLVTLLPLLNMAYKFRT.S.ETLEQLYPWECFVFCLTIFGTFTNQIHKWSHTYLGLP.WV
Retrocopy HDFIETNEDNCLVTLLPLLNMAYKFRTHSSETLEQLYPWECFVFCLTIFGTFTNQIHKWSHTYLGLPCWV

Parental  TVLQDWHVILPRKHHRIHHVAPHETYFCITTGWLNYPLEVIGFWRRLEDLIQGLTGEKPRADDMKWAQKI
          TVLQDWHVILPRKH..IHHVA.HET.FCITTGWLNY..EVIGFWRRLEDLIQGLTGEKPRADDMKWAQKI
Retrocopy TVLQDWHVILPRKHRCIHHVAAHETSFCITTGWLNYRPEVIGFWRRLEDLIQGLTGEKPRADDMKWAQKI

Parental  K
          K
Retrocopy K

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	17.01 RPM
SRP007412_cerebellum	0.00 RPM	17.28 RPM
SRP007412_heart	0.00 RPM	17.93 RPM
SRP007412_kidney	0.13 RPM	85.08 RPM
SRP007412_liver	0.00 RPM	9.15 RPM
SRP007412_testis	1.05 RPM	22.37 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2219 was not detected

EST

No EST(s) were mapped for retro_mmus_2219 retrocopy.

TSS

No TSS is located nearby retro_mmus_2219 retrocopy 5' end.

Lab

retro_mmus_2219 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2219 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,