RetrogeneDB ID: retro_mmus_919

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:13436678..13437098(-)
• Located in intron of: ENSMUSG00000020576

Retrocopy information

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

Parental gene information

• Parental gene symbol: Derl1
• Ensembl ID: ENSMUSG00000022365
• Aliases: Derl1, 1110021N07Rik, AI195141, AW551338, Derlin-1
• Description: Der1-like domain family, member 1 [Source:MGI Symbol;Acc:MGI:1915069]

Sequence

>retro_mmus_919
ATGTCGGACATCGGGGACTGGTTCAGGAGCATCCCGGCCATCACACACTACTGGTTTGCTGCTACGGTTGCTGTCCCCTT
CTTGATCTGCAAGCTCGGCATCATCAGCCCGGCCTACTTCTTCCTCTGGCCCGAAGCCTTCCTCTATCGCTTCCAGATAT
GGAGGCCGTTCACTGCCACCTTTTACTTCCCCGTGGGCCCAGGGACTGGATTTCTGTATTTGGTCAATTTATATTTCTTA
TATCAGTATTCTACGCGGCTTGAAGCAGGAGCTTTTGACGGGAGGCCAGCAGACTATTTATTCATGCTTCTCTTTAACTG
GATCTGCATCGTTATTACTGGCTTAGCAATGGATATGCAGCTGCTGCTGATCCCTCTGATCATGTCAGTGCTCTACGTCT
GAGCCCAGCTGAACAGAGAG

Alignment

ORF - retro_mmus_919 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.71 %
• Parental protein coverage: 55.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDIGDWFRSIPAITRYWFAATVAVP-LIGKLGIISPAYFFLWPEAFLYRFQIWRPFTATFYFPVGPGTG
          MSDIGDWFRSIPAIT.YWFAATVAVP.LI.KLGIISPAYFFLWPEAFLYRFQIWRPFTATFYFPVGPGTG
Retrocopy MSDIGDWFRSIPAITHYWFAATVAVPFLICKLGIISPAYFFLWPEAFLYRFQIWRPFTATFYFPVGPGTG

Parental  FLYLVNLYFLYQYSTRLEAGAFDGRPADYLFMLLFNWICIVITGLAMDMQLLMIPLIMSVLYVWAQLNRD
          FLYLVNLYFLYQYSTRLEAGAFDGRPADYLFMLLFNWICIVITGLAMDMQLL.IPLIMSVLYV.AQLNR.
Retrocopy FLYLVNLYFLYQYSTRLEAGAFDGRPADYLFMLLFNWICIVITGLAMDMQLLLIPLIMSVLYV*AQLNRE

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	0.35 RPM	43.46 RPM
SRP007412_cerebellum	0.22 RPM	51.58 RPM
SRP007412_heart	1.09 RPM	43.68 RPM
SRP007412_kidney	0.60 RPM	62.98 RPM
SRP007412_liver	1.75 RPM	84.00 RPM
SRP007412_testis	0.55 RPM	31.38 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_919 was not detected

EST

No EST(s) were mapped for retro_mmus_919 retrocopy.

TSS

No TSS is located nearby retro_mmus_919 retrocopy 5' end.

Lab

retro_mmus_919 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_919 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006519	1 retrocopy	retro_amel_364,
Canis familiaris	ENSCAFG00000000974	1 retrocopy	retro_cfam_754,
Cavia porcellus	ENSCPOG00000011870	1 retrocopy	retro_cpor_1520,
Myotis lucifugus	ENSMLUG00000009085	1 retrocopy	retro_mluc_2035,
Mustela putorius furo	ENSMPUG00000001132	1 retrocopy	retro_mputfur_1082,
Mus musculus	ENSMUSG00000022365	1 retrocopy	retro_mmus_919 ,
Rattus norvegicus	ENSRNOG00000005551	2 retrocopies	retro_rnor_1206, retro_rnor_2717,
Sarcophilus harrisii	ENSSHAG00000011915	1 retrocopy	retro_shar_588,