RetrogeneDB ID: retro_mmus_988

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:3352974..3353988(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rrm2b
• Ensembl ID: ENSMUSG00000022292
• Aliases: Rrm2b, p53R2
• Description: ribonucleotide reductase M2 B (TP53 inducible) [Source:MGI Symbol;Acc:MGI:2155865]

Sequence

>retro_mmus_988
CGGCCAGGCCAGGGTGAGCAATTGTGTTCAGAGACAGAAGAAAATGTGGTGAGGTCAAATGAAGAGCCGCTCCTAAGAAA
GAGTTCCCGAAGGTTTGTCATCTTTCCAATCCAGTATCCTGATATCTGGAGAATGTATAAGCAAGCACGGGCATCTTTCT
GGACAGGAGAAGAGGTTGACTTGTCAAAGAACCTCCCTCACTGGAACAAGCTTAAATCCGACGAGAAGTATTTTATCTCC
CACATCTTAGCCTTTTTTGCAGCCAGTGATGGAATTGTAAATGAAAACTTGGTGGAGCGTTTTAGTCAGGAGGTCCAGGT
TCCGGAGACTCACTGCTTCTATGGCTTTCAGATTCTCATCGAGAATGTTCACTCAGAGATGTACAGTTTACTAATAGACA
CTTACATCAGAGATCCAAAGAAAAGGGAATTTTTATTTAACGCAATTGAAACAATGCCATATGTTAAGAAAAAAGCAGAC
TAGGCTCTGCGCTGGATAGCAGATAGGAAATCTACTTTTGGGGAAAGAGTGGTGGCCTTTGCTGCTGTGGAAGGAATTTC
CTTCTCTGGATCATTTGCTGCAATATTCTGGCTAAAGAAGAGAGGCCTCATGCCTGGACTGACTTTTTCAAATGAACTGA
TCAGCAGGGATGAAGGTCTTCACTGTGACTTTGCCTGCCTGATGTTTCAGTACAAGCCTTCAGAAGACAGAGTGAGGGAA
ATCATTGCTGATGCTGTTCAAATTGAGCAGGAGTTTTTAACAGAAGCCTTGCCTGTTGGCCTCATTGGAATGAACTGTGT
TTTGACGAAACAGTACATTGAGTTTGTAGCTGACAGATTACTTGTAGAACTTGGATTCTCAAAGATTTTTCAGGCAGAAA
ATCCCTTTGATTTTATGGAGAACATTTCATTAGAAGGGAAAACAAATTTCTTTGAGAAACGAGTTTCTGAGTATCAGAGA
TTTGCAGTCATGGCGGAAACCACCGATAATGTCTTCACCTTGGATGCAGATTTC

Alignment

ORF - retro_mmus_988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.89 %
• Parental protein coverage: 97.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RPEKGEQLCSETEENVVRSNEEPLLRKSSRRFVIFPIQYPDIWRMYKQAQASFWTAEEVDLSKDLPHWNK
          RP..GEQLCSETEENVVRSNEEPLLRKSSRRFVIFPIQYPDIWRMYKQA.ASFWT.EEVDLSK.LPHWNK
Retrocopy RPGQGEQLCSETEENVVRSNEEPLLRKSSRRFVIFPIQYPDIWRMYKQARASFWTGEEVDLSKNLPHWNK

Parental  LKSDEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPK
          LKSDEKYFISHILAFFAASDGIVNENLVERFSQEVQVPE..CFYGFQILIENVHSEMYSLLIDTYIRDPK
Retrocopy LKSDEKYFISHILAFFAASDGIVNENLVERFSQEVQVPETHCFYGFQILIENVHSEMYSLLIDTYIRDPK

Parental  KREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGIFFSGSFAAIFWLKKRGLMPGLTFS
          KREFLFNAIETMPYVKKKAD.ALRWIADRKSTFGERVVAFAAVEGI.FSGSFAAIFWLKKRGLMPGLTFS
Retrocopy KREFLFNAIETMPYVKKKAD*ALRWIADRKSTFGERVVAFAAVEGISFSGSFAAIFWLKKRGLMPGLTFS

Parental  NELISRDEGLHCDFACLMFQYLVNKPSEDRVREIIADAVQIEQEFLTEALPVGLIGMNCVLMKQYIEFVA
          NELISRDEGLHCDFACLMFQY...KPSEDRVREIIADAVQIEQEFLTEALPVGLIGMNCVL.KQYIEFVA
Retrocopy NELISRDEGLHCDFACLMFQY---KPSEDRVREIIADAVQIEQEFLTEALPVGLIGMNCVLTKQYIEFVA

Parental  DRLLGELGFSKIFQAENPFDFMENISLEGKTNFFEKRVSEYQRFAVMAETTDNVFTLDADF
          DRLL.ELGFSKIFQAENPFDFMENISLEGKTNFFEKRVSEYQRFAVMAETTDNVFTLDADF
Retrocopy DRLLVELGFSKIFQAENPFDFMENISLEGKTNFFEKRVSEYQRFAVMAETTDNVFTLDADF

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	0.09 RPM	26.31 RPM
SRP007412_cerebellum	0.00 RPM	16.15 RPM
SRP007412_heart	0.00 RPM	24.53 RPM
SRP007412_kidney	0.04 RPM	23.68 RPM
SRP007412_liver	0.00 RPM	3.74 RPM
SRP007412_testis	0.09 RPM	2.74 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_988 was not detected

EST

No EST(s) were mapped for retro_mmus_988 retrocopy.

TSS

No TSS is located nearby retro_mmus_988 retrocopy 5' end.

Lab

retro_mmus_988 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_988 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012265	4 retrocopies	retro_chof_1118, retro_chof_1233, retro_chof_277, retro_chof_692,
Callithrix jacchus	ENSCJAG00000015923	1 retrocopy	retro_cjac_4130,
Echinops telfairi	ENSETEG00000020338	1 retrocopy	retro_etel_1219,
Gorilla gorilla	ENSGGOG00000003053	1 retrocopy	retro_ggor_3001,
Mus musculus	ENSMUSG00000020649	2 retrocopies	retro_mmus_2472, retro_mmus_3073,
Mus musculus	ENSMUSG00000022292	1 retrocopy	retro_mmus_988 ,
Otolemur garnettii	ENSOGAG00000004487	1 retrocopy	retro_ogar_2602,
Pan troglodytes	ENSPTRG00000020481	1 retrocopy	retro_ptro_3204,
Ictidomys tridecemlineatus	ENSSTOG00000008543	2 retrocopies	retro_itri_1555, retro_itri_877,
Tupaia belangeri	ENSTBEG00000008855	1 retrocopy	retro_tbel_3693,