RetrogeneDB ID: retro_mmus_1968

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:127204761..127205168(+)
• Located in intron of: ENSMUSG00000044145

Retrocopy information

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

Parental gene information

• Parental gene symbol: Utp11l
• Ensembl ID: ENSMUSG00000028907
• Aliases: None
• Description: UTP11-like, U3 small nucleolar ribonucleoprotein, (yeast) [Source:MGI Symbol;Acc:MGI:1914455]

Sequence

>retro_mmus_1968
ATATCGGTGGCTTTTCCCAAGGTTGCCAAGACCCGGCAGCGAGAACACAAGAGAACGAAGCCAGCCTGGCTTTTGAAAAC
ACCTGGGTTCTGGAAAAAAAGAAAGATTACAAACTTCGAGCAAATGACCATCATAAAAAACAAGATTTCTTCACAATTCT
CTGGAAGAAGGCTCTTGAAAAAATTTCAGAAGAATTCTACATTAAAGTGACTCCGGCCAAAATCCAGGATGGAGTTCGTA
TTTTTAAAGAGAGCAAGGAAGAAGTAACAGCTGAGCAGCTAAGCTGATGAGAACTCAGAACATCAAGTACATAGAGAGGA
AAAGGATTGCAGAAGCAAAGAAAATTGAAAGACTGAAATCAGAGCGCCATCTGCTGGATTTCCAGGGAGAAGCAGCAGAA
TAAGCAC

Alignment

ORF - retro_mmus_1968 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.66 %
• Parental protein coverage: 53.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSAAFRKAAKTRQREHRERSQPGFRKRLG-LLEKKKDYKLRANDYHKKQDFLRALRKKALEKNPDEFYYK
          .S.AF.K.AKTRQREH.........K..G..LEKKKDYKLRAND.HKKQDF...L.KKALEK...EFY.K
Retrocopy ISVAFPKVAKTRQREHKRTKPAWLLKTPG<VLEKKKDYKLRANDHHKKQDFFTILWKKALEKISEEFYIK

Parental  MTRAKLQDGVHIFKENKEEVTAEQL-KLMRTQDIKYIEMKRVAEAKKIERLKSELHLLDFQG-KQQKKH
          .T.AK.QDGV.IFKE.KEEVTAEQL.KLMRTQ.IKYIE.KR.AEAKKIERLKSE.HLLDFQG.KQQ.KH
Retrocopy VTPAKIQDGVRIFKESKEEVTAEQL<KLMRTQNIKYIERKRIAEAKKIERLKSERHLLDFQG>KQQNKH

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	0.19 RPM	15.82 RPM
SRP007412_cerebellum	0.09 RPM	21.58 RPM
SRP007412_heart	0.16 RPM	16.75 RPM
SRP007412_kidney	0.60 RPM	28.14 RPM
SRP007412_liver	0.71 RPM	19.74 RPM
SRP007412_testis	0.14 RPM	13.58 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1968 was not detected

EST

No EST(s) were mapped for retro_mmus_1968 retrocopy.

TSS

No TSS is located nearby retro_mmus_1968 retrocopy 5' end.

Lab

retro_mmus_1968 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1968 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001043	1 retrocopy	retro_cpor_1084,
Microcebus murinus	ENSMICG00000001496	1 retrocopy	retro_mmur_894,
Myotis lucifugus	ENSMLUG00000001003	1 retrocopy	retro_mluc_2386,
Mus musculus	ENSMUSG00000028907	1 retrocopy	retro_mmus_1968 ,
Oryctolagus cuniculus	ENSOCUG00000007154	2 retrocopies	retro_ocun_1285, retro_ocun_669,
Otolemur garnettii	ENSOGAG00000016492	2 retrocopies	retro_ogar_3229, retro_ogar_3324,
Rattus norvegicus	ENSRNOG00000007174	1 retrocopy	retro_rnor_1838,