RetrogeneDB ID: retro_mmus_3214

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:73749474..73750161(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cr1l
• Ensembl ID: ENSMUSG00000016481
• Aliases: Cr1l, Crry, Mcp, mCRY
• Description: complement component (3b/4b) receptor 1-like [Source:MGI Symbol;Acc:MGI:88513]

Sequence

>retro_mmus_3214
TTATACTGTACCAGCAACGATGGTGAAATTGGAGTCTGGAGTGGCCCTCCTCCTCAGTGCATTGGATTCAACAAATGTAC
TCCTCCTCCCTATGTTGAAAATGCAGTCATGCTGTCTGAGAACAGAAGCTTGTTTTCCTTAAGGGATATTGTGGAGTTTA
GATGTCACCCTGGCTTTATCATGAAAGGAGCCAGCAGTGTGCATTGTCAGTCCCTAAACAAATGGGAGCCAGAGTTACCA
AGCTGCTTCAAGGGAGTGATATGTCGTCTCCCTCAGGAGATGAGTGGATTCCAGAAGGGGTTGGGAATGAAAAAAGAATA
TTATTATGGAGAGAATGTAACCTTGGAATGCGAGGATGGGTATACTGTAGAAGGCAGTTCTCAAAGCCAGTGTCAGTCTG
ATGGCAGCTGGAATCCTCTTCTGGCCAAAAGTGTATCGCGCTCAATCAGTGGTCTAATTGTTGGAATTTTCATTGGGATG
ATCATCTTTATTTTATTCATCATTGTTTTCATTTGGATGATTCTGAAGTATAAAAAACGCAATACCACAGATGAAAAGTA
TAAAGAAGTGGGTATTCATTTAAATTATAAAGGAGACAGCTGTGTCTGCCTTCAGTCTCTGCTCATAAGTCAGGAGAACA
GCACTACCACTAGCCCAGCACAGAATTCACTCGCTCAAGAAGTCTCC

Alignment

ORF - retro_mmus_3214 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.32 %
• Parental protein coverage: 52.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LYCTSNDGEIGVWSGPPPQCIELNKCTPPPYVENAVMLSENRSLFSLRDIVEFRCHPGFIMKGASSVHCQ
          LYCTSNDGEIGVWSGPPPQCI..NKCTPPPYVENAVMLSENRSLFSLRDIVEFRCHPGFIMKGASSVHCQ
Retrocopy LYCTSNDGEIGVWSGPPPQCIGFNKCTPPPYVENAVMLSENRSLFSLRDIVEFRCHPGFIMKGASSVHCQ

Parental  SLNKWEPELPSCFKGVICRLPQEMSGFQKGLGMKKEYYYGENVTLECEDGYTLEGSSQSQCQSDGSWNPL
          SLNKWEPELPSCFKGVICRLPQEMSGFQKGLGMKKEYYYGENVTLECEDGYT.EGSSQSQCQSDGSWNPL
Retrocopy SLNKWEPELPSCFKGVICRLPQEMSGFQKGLGMKKEYYYGENVTLECEDGYTVEGSSQSQCQSDGSWNPL

Parental  LAKCVSRSISGLIVGIFIGIIVFILVIIVFIWMILKYKKRNTTDEKYKEVGIHLNYKEDSCVRLQSLLTS
          LAK.VSRSISGLIVGIFIG.I.FIL.IIVFIWMILKYKKRNTTDEKYKEVGIHLNYK.DSCV.LQSLL.S
Retrocopy LAKSVSRSISGLIVGIFIGMIIFILFIIVFIWMILKYKKRNTTDEKYKEVGIHLNYKGDSCVCLQSLLIS

Parental  QENSSTTSPARNSLTQEVS
          QENS.TTSPA.NSL.QEVS
Retrocopy QENSTTTSPAQNSLAQEVS

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	8.18 RPM
SRP007412_cerebellum	0.00 RPM	7.77 RPM
SRP007412_heart	0.12 RPM	29.48 RPM
SRP007412_kidney	0.19 RPM	25.04 RPM
SRP007412_liver	0.08 RPM	25.01 RPM
SRP007412_testis	0.05 RPM	2.38 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3214 was not detected

EST

No EST(s) were mapped for retro_mmus_3214 retrocopy.

TSS

No TSS is located nearby retro_mmus_3214 retrocopy 5' end.

Lab

retro_mmus_3214 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3214 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
Mus musculus	ENSMUSG00000016481	1 retrocopy	retro_mmus_3214 ,
Mus musculus	ENSMUSG00000090623	1 retrocopy	retro_mmus_492,