RetrogeneDB ID: retro_mmus_1331

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:19756403..19756819(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Polr2d
• Ensembl ID: ENSMUSG00000024258
• Aliases: Polr2d, 2310002G05Rik, 2610028L19Rik, HSRBP4, RBP4
• Description: polymerase (RNA) II (DNA directed) polypeptide D [Source:MGI Symbol;Acc:MGI:1916491]

Sequence

>retro_mmus_1331
GGTGGAAGTTGTCCTCTGGCTGGTGACATAGAAGAAGATGCTTCACAGCTCATCTTTCCCAAAGAGTTTGAAATAACTGA
AGCACTCCTAAACTCTGAAGTTCACAGGCTTCTGGAGCATCGAAAGCAGCAGAATGAGAACTAGGAAGACAAGCGGAAGC
TTCCAGAGGTATTCATGAAAACCCTGAACTATACAGTCCGTTTCAGGCGATTCAAAAACAAGAGACCATTGCCAGTGTCC
GTAGCTTGCTTCTCCAGAAAAAGCTACATAAGTTTGAGTTAGCCTGCTTACCCAGTCTTTGCTGGGAGTCTGCTGAAGAG
TCCAAAGCTCTGATTCCAAGCCTGAAAGGGCGTTTTGAAGGTGAGGAACTACAGCAGATTCTCAATGATATCCAGACGAA
GCACAGCTTCCAGTAC

Alignment

ORF - retro_mmus_1331 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.14 %
• Parental protein coverage: 97.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSR
          GGS.P.AGD.EEDASQLIFPKEFE..E.LLNSEVH.LLEHRKQQNE..ED...L.EVFMKTLNYT.RF.R
Retrocopy GGSCPLAGDIEEDASQLIFPKEFEITEALLNSEVHRLLEHRKQQNEN*EDKRKLPEVFMKTLNYTVRFRR

Parental  FKNR-ETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDIQTKRSFQY
          FKN..ETIASVRSLLLQKKLHKFELACL..LC.E.AEESKALIPSL.GRFE.EELQQIL.DIQTK.SFQY
Retrocopy FKNK<ETIASVRSLLLQKKLHKFELACLPSLCWESAEESKALIPSLKGRFEGEELQQILNDIQTKHSFQY

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	10.65 RPM
SRP007412_cerebellum	0.00 RPM	15.02 RPM
SRP007412_heart	0.00 RPM	14.38 RPM
SRP007412_kidney	0.00 RPM	14.78 RPM
SRP007412_liver	0.00 RPM	4.34 RPM
SRP007412_testis	0.00 RPM	11.25 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1331 was not detected

EST

No EST(s) were mapped for retro_mmus_1331 retrocopy.

TSS

No TSS is located nearby retro_mmus_1331 retrocopy 5' end.

Lab

retro_mmus_1331 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1331 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011746	1 retrocopy	retro_amel_1020,
Canis familiaris	ENSCAFG00000004311	2 retrocopies	retro_cfam_1403, retro_cfam_2188,
Choloepus hoffmanni	ENSCHOG00000013850	3 retrocopies	retro_chof_1003, retro_chof_1568, retro_chof_1920,
Dasypus novemcinctus	ENSDNOG00000008527	1 retrocopy	retro_dnov_734,
Felis catus	ENSFCAG00000027816	1 retrocopy	retro_fcat_1148,
Gorilla gorilla	ENSGGOG00000004723	1 retrocopy	retro_ggor_1658,
Macaca mulatta	ENSMMUG00000001989	1 retrocopy	retro_mmul_1011,
Monodelphis domestica	ENSMODG00000018653	4 retrocopies	retro_mdom_1320, retro_mdom_457, retro_mdom_689, retro_mdom_851,
Mustela putorius furo	ENSMPUG00000016685	1 retrocopy	retro_mputfur_611,
Mus musculus	ENSMUSG00000024258	1 retrocopy	retro_mmus_1331 ,
Oryctolagus cuniculus	ENSOCUG00000021449	1 retrocopy	retro_ocun_35,
Ochotona princeps	ENSOPRG00000005327	2 retrocopies	retro_opri_233, retro_opri_725,
Pongo abelii	ENSPPYG00000012759	1 retrocopy	retro_pabe_1933,
Pan troglodytes	ENSPTRG00000012436	1 retrocopy	retro_ptro_1571,
Sorex araneus	ENSSARG00000009037	1 retrocopy	retro_sara_420,
Sarcophilus harrisii	ENSSHAG00000014817	1 retrocopy	retro_shar_728,
Ictidomys tridecemlineatus	ENSSTOG00000023329	3 retrocopies	retro_itri_1323, retro_itri_145, retro_itri_600,