RetrogeneDB ID: retro_mmus_1681

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:4010440..4011157(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rhbdl2
• Ensembl ID: ENSMUSG00000043333
• Aliases: Rhbdl2, 9130416B15, RRP2
• Description: rhomboid, veinlet-like 2 (Drosophila) [Source:MGI Symbol;Acc:MGI:3608413]

Sequence

>retro_mmus_1681
AGAGCCAACTGCCTCCCGCCGCCCCTGTTCATCATCCTCATCAGTCTGGCTGAGCTGGCTGTGTTTATTTATTATGCGGT
GTGGAAGCCACAGAAGCAGTGGATCATCCTGGACACGGGGATCTTGGAAAGTCCCTTGACATACTGCTCTGAGAAGAGGG
GGGAAGCCTGCAGGTTTATCTCATACATGCTGGTCCATGCCGGAGTCCAGCACATCGTGGGGAATCTTTTTATGCAGATC
ATCCTGGGTATTCCTTTGGAAATGGTCCACAAAGGCCTCCGAGTAGGGCTGGTGTGCCTAGCAGGAGTGCTTGCAGGTTC
CCTGGCCAGCTCCATCTTTGACCCCCTTAAGTCTCTTGTGGGAGCTTCAGGAGGAGTCTATGCATTGATGGGAGGATATT
TTATGAATGTTATAGTGAACTTTAGAGAAATGATTCCTGCCTTTGGAATTGTCAGACTACTCGTTATCATTCTGATAGTT
GCGTCAGACATGGGATTTGCTCTCTACAGAAGATTCTTTGTCCCTGCAAATGGGTCTCCGGTGTCCTTTGCTGCTCACAT
TGCAGGCGGATTTGCTGGGATGTCCATAGGTTACTCTGTGTTCAGCTGCTTTGACAAGACCCTGCTCAAAGATCCCAGGT
TCTGGATCGCAATTGCTGCATATGTAGCTTCTCTCTTATTTGCTGTGTTTTTTAACATCTTTCTGTCCCCAGCAAAC

Alignment

ORF - retro_mmus_1681 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.23 %
• Parental protein coverage: 79.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RANCLPPPLFIILISLAELAVFIYYAVWKPQKQWITLDTGILESPLTYCPEKREEAWRFISYMLVHAGVQ
          RANCLPPPLFIILISLAELAVFIYYAVWKPQKQWI.LDTGILESPLTYC.EKR.EA.RFISYMLVHAGVQ
Retrocopy RANCLPPPLFIILISLAELAVFIYYAVWKPQKQWIILDTGILESPLTYCSEKRGEACRFISYMLVHAGVQ

Parental  HIVGNLLMQIVLGIPLEMVHKGLRVGLVYLAGVLAGSLASSIFDPLKSLVGASGGVYALMGGYFMNVIVN
          HIVGNL.MQI.LGIPLEMVHKGLRVGLV.LAGVLAGSLASSIFDPLKSLVGASGGVYALMGGYFMNVIVN
Retrocopy HIVGNLFMQIILGIPLEMVHKGLRVGLVCLAGVLAGSLASSIFDPLKSLVGASGGVYALMGGYFMNVIVN

Parental  FREMIPAFGIVRLLVIILIVASDMGFALYRRFFVPANGSPVSFAAHIAGGFAGMSIGYTVFSCFDKTLLK
          FREMIPAFGIVRLLVIILIVASDMGFALYRRFFVPANGSPVSFAAHIAGGFAGMSIGY.VFSCFDKTLLK
Retrocopy FREMIPAFGIVRLLVIILIVASDMGFALYRRFFVPANGSPVSFAAHIAGGFAGMSIGYSVFSCFDKTLLK

Parental  DPRFWIAIAAYVACLLFAVFFNIFLSPAN
          DPRFWIAIAAYVA.LLFAVFFNIFLSPAN
Retrocopy DPRFWIAIAAYVASLLFAVFFNIFLSPAN

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	0.23 RPM
SRP007412_cerebellum	0.00 RPM	0.39 RPM
SRP007412_heart	0.03 RPM	0.12 RPM
SRP007412_kidney	0.00 RPM	1.31 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	1.19 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1681 was not detected

EST

No EST(s) were mapped for retro_mmus_1681 retrocopy.

TSS

No TSS is located nearby retro_mmus_1681 retrocopy 5' end.

Lab

retro_mmus_1681 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1681 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mustela putorius furo	ENSMPUG00000014455	1 retrocopy	retro_mputfur_1373,
Mus musculus	ENSMUSG00000043333	1 retrocopy	retro_mmus_1681 ,