RetrogeneDB ID: retro_mmus_1260

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:31458827..31459182(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Prelid2
• Ensembl ID: ENSMUSG00000056671
• Aliases: Prelid2, 1700003A01Rik, C330008K14Rik
• Description: PRELI domain containing 2 [Source:MGI Symbol;Acc:MGI:1924869]

Sequence

>retro_mmus_1260
GAGCAGGTGGTCGCTTGCTTCCTCTGAAAGGTGAGTATTTTAAAGGTACCTGATAATCCAGCTAGAAGAAGAGTCATGGC
TGAGCCTTCAGAAAAGGAACATGGCTATCCGGAGTCGCTGCCTCACGTGGACACAGTACGCATCCTTGAAGGAAGCGTCT
GTCTTCCGGGAAAGCATAGAAAGTCCAGGTTGGACAGAGTTCATTCAAACAGGCAGAATTCCAGTCACAGCGGCTGAATT
TCTCAACTGTGTTTTGGAGACTTTTGCTAGAACGTTCTTAAGACAAGGAGCCCAGAAGGGAATTAGAATATTGGAGATGC
TGCTAAAGGAACAGTGTGGCTCCCCCTTAGTGGAA

Alignment

ORF - retro_mmus_1260 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QNVVPEILRKVSILKVPD-IQLEEESWLSLQKRNMAIRSHCLTWTQYASMREESVFRESVENPNWTEFIQ
          ..VV...L.KVSILKVPD.IQLEEESWLSLQKRNMAIRS.CLTWTQYAS..E.SVFRES.E.P.WTEFIQ
Retrocopy EQVVACFL*KVSILKVPD>IQLEEESWLSLQKRNMAIRSRCLTWTQYASLKEASVFRESIESPGWTEFIQ

Parental  TGRISITGAGFLNCILETFASTFLRQGAQKGIRIMEMLLKEQCGSPLVE
          TGRI..T.A.FLNC.LETFA.TFLRQGAQKGIRI.EMLLKEQCGSPLVE
Retrocopy TGRIPVTAAEFLNCVLETFARTFLRQGAQKGIRILEMLLKEQCGSPLVE

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	0.05 RPM	0.07 RPM
SRP007412_cerebellum	0.09 RPM	0.17 RPM
SRP007412_heart	0.00 RPM	2.52 RPM
SRP007412_kidney	0.04 RPM	2.85 RPM
SRP007412_liver	0.03 RPM	1.47 RPM
SRP007412_testis	0.50 RPM	0.41 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1260 was not detected

EST

No EST(s) were mapped for retro_mmus_1260 retrocopy.

TSS

No TSS is located nearby retro_mmus_1260 retrocopy 5' end.

Lab

retro_mmus_1260 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1260 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001222	1 retrocopy	retro_cpor_821,
Echinops telfairi	ENSETEG00000005000	2 retrocopies	retro_etel_1464, retro_etel_1676,
Homo sapiens	ENSG00000186314	1 retrocopy	retro_hsap_1134,
Macaca mulatta	ENSMMUG00000013588	1 retrocopy	retro_mmul_877,
Mus musculus	ENSMUSG00000056671	1 retrocopy	retro_mmus_1260 ,
Nomascus leucogenys	ENSNLEG00000009800	1 retrocopy	retro_nleu_928,
Otolemur garnettii	ENSOGAG00000010025	2 retrocopies	retro_ogar_2400, retro_ogar_2477,
Pan troglodytes	ENSPTRG00000017368	1 retrocopy	retro_ptro_770,
Tursiops truncatus	ENSTTRG00000016708	1 retrocopy	retro_ttru_1875,