RetrogeneDB ID: retro_mmus_540

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:27870171..27870717(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: U2af1l4
• Ensembl ID: ENSMUSG00000078765
• Aliases: U2af1l4, AA407033, AF419339, AI451269, AW553050, U2af26
• Description: U2 small nuclear RNA auxiliary factor 1-like 4 [Source:MGI Symbol;Acc:MGI:2678374]

Sequence

>retro_mmus_540
AAACTGACTTTCAGCCAGACAATAGTCCTGCTCAACTTGTACCGGAATCCATAGAACACAGCCCAAACTACAGATGGATC
ACACTGTCATGTGAGCGATGTGGAGGTGCAAGAACACTATGATACCTTCTTTGAGGAGGTATTCACAGAACTGCAGGAGA
ACTATGGAAAGATTGAAGAGAGGAATGTGTGTGACAACCTTGGGGACCACCTCGTGGGCAATGTCTATGTTAAGTTCCGG
CAGGAGGAGGATGCAGAGTGGGCTGTGGCAGAACTCAATAACCGCTGATTCAACAGGTAGGCTGTGCATGCTGAGCTGTC
TCCTGTCACTGACTCCCAAGAATTGTGCTTCAGGCTGTATGACATGAAGGAATGCACCTGAGGTGGCTTCTGCAATTTTA
TGCATCTACGACCCATATCCTGGAACTTGCACTGGCAGCTCTATGGGCAAAGACTCAGGCATAGGTCACCTCCAAGGTCC
CATACAGGTCACCATCCCCGAGAAAAGAACAGATGTTGTTCCCCAGACTACCCTTCTAGTCCCTTC

Alignment

ORF - retro_mmus_540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.77 %
• Parental protein coverage: 82.73 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KPTFSQTIVLLNLYRNPQNTAQTADGSHCHVSDVEVQEHYDNFFEEVFTELQEKYGEIEEMNVCDNLGDH
          K.TFSQTIVLLNLYRNP.NTAQT.DGSHCHVSDVEVQEHYD.FFEEVFTELQE.YG.IEE.NVCDNLGDH
Retrocopy KLTFSQTIVLLNLYRNP*NTAQTTDGSHCHVSDVEVQEHYDTFFEEVFTELQENYGKIEERNVCDNLGDH

Parental  LVGNVYVKFRREEDAERAVAELNNRWFNGQAVHAELSPVTDFRESCCRQYEMGECTRGGFCNFMHLRPIS
          LVGNVYVKFR.EEDAE.AVAELNNR.FN..AVHAELSPVTD..E.C.R.Y.M.ECT.GGFCNFMHLRPIS
Retrocopy LVGNVYVKFRQEEDAEWAVAELNNR*FNR*AVHAELSPVTDSQELCFRLYDMKECT*GGFCNFMHLRPIS

Parental  RNLRRQLYGRGPRHRSPPRSHTGHRPRERNRRRSPDHRHGRF
          .NL..QLYG...RHRSPPRSHTGH.PRE.NR..SPD.....F
Retrocopy WNLHWQLYGQRLRHRSPPRSHTGHHPREKNRCCSPDYPSSPF

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	16.77 RPM
SRP007412_cerebellum	0.00 RPM	31.26 RPM
SRP007412_heart	0.00 RPM	23.44 RPM
SRP007412_kidney	0.00 RPM	17.57 RPM
SRP007412_liver	0.00 RPM	11.01 RPM
SRP007412_testis	0.00 RPM	16.01 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_540 was not detected

EST

No EST(s) were mapped for retro_mmus_540 retrocopy.

TSS

No TSS is located nearby retro_mmus_540 retrocopy 5' end.

Lab

retro_mmus_540 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_540 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000006383	1 retrocopy	retro_fcat_1650,
Gorilla gorilla	ENSGGOG00000016828	1 retrocopy	retro_ggor_150,
Loxodonta africana	ENSLAFG00000012923	1 retrocopy	retro_lafr_1090,
Mus musculus	ENSMUSG00000031370	1 retrocopy	retro_mmus_233,
Mus musculus	ENSMUSG00000061613	3 retrocopies	retro_mmus_1602, retro_mmus_1787, retro_mmus_2955,
Mus musculus	ENSMUSG00000078765	1 retrocopy	retro_mmus_540 ,
Oryctolagus cuniculus	ENSOCUG00000013434	1 retrocopy	retro_ocun_1184,
Sus scrofa	ENSSSCG00000002896	1 retrocopy	retro_sscr_543,