RetrogeneDB ID: retro_mmus_2287

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:107999486..107999707(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Polr2i
• Ensembl ID: ENSMUSG00000019738
• Aliases: Polr2i, 2810002B19Rik
• Description: polymerase (RNA) II (DNA directed) polypeptide I [Source:MGI Symbol;Acc:MGI:1917170]

Sequence

>retro_mmus_2287
AATAACATGTTGTACCCCAAGGAGGACAAGGAACCACATTCTGCGATAAGCGTGCCAGAATTGTAAACTACCAGCAGGAA
GCAGAAAACAGCTGCATCTACATCAACAGAATCACTCACAAGTAGACAGGCTGAACCAGATCATTGCAGACATGTCCCAG
GAACCTATGATGATGAGGACCAAAGACCACCCCGTATCAGAAGTGTGGCTACAAGGATAGT

Alignment

ORF - retro_mmus_2287 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.54 %
• Parental protein coverage: 59.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NNMLY-PKEDKENRILLYACRNC-DYQQEADNSCIYVNKITH-EVDELTQIIADVSQDPTLPRTEDHPC-
          NNMLY.P.....N.IL..AC.NC..YQQEA.NSCIY.N.ITH..VD.L.QIIAD.SQ.P...RT.DHP..
Retrocopy NNMLY>PRRTR-NHILR*ACQNC>NYQQEAENSCIYINRITH<QVDRLNQIIADMSQEPMMMRTKDHPV>

Parental  QKCGHKEA
          QKCG.K..
Retrocopy QKCGYKDS

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	10.33 RPM
SRP007412_cerebellum	0.00 RPM	20.19 RPM
SRP007412_heart	0.00 RPM	19.30 RPM
SRP007412_kidney	0.02 RPM	21.06 RPM
SRP007412_liver	0.00 RPM	20.86 RPM
SRP007412_testis	0.00 RPM	37.73 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2287 was not detected

EST

No EST(s) were mapped for retro_mmus_2287 retrocopy.

TSS

No TSS is located nearby retro_mmus_2287 retrocopy 5' end.

Lab

retro_mmus_2287 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2287 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006601	1 retrocopy	retro_cfam_1400,
Callithrix jacchus	ENSCJAG00000009671	1 retrocopy	retro_cjac_2777,
Dipodomys ordii	ENSDORG00000001852	2 retrocopies	retro_dord_264, retro_dord_555,
Monodelphis domestica	ENSMODG00000014172	1 retrocopy	retro_mdom_1465,
Mus musculus	ENSMUSG00000019738	1 retrocopy	retro_mmus_2287 ,
Oryctolagus cuniculus	ENSOCUG00000013044	2 retrocopies	retro_ocun_103, retro_ocun_1603,
Otolemur garnettii	ENSOGAG00000024254	1 retrocopy	retro_ogar_386,
Ochotona princeps	ENSOPRG00000001789	2 retrocopies	retro_opri_350, retro_opri_837,
Tursiops truncatus	ENSTTRG00000003919	1 retrocopy	retro_ttru_223,