RetrogeneDB ID: retro_mmus_383

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:161821862..161822402(+)
• Located in intron of: ENSMUSG00000040297

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cdk7
• Ensembl ID: ENSMUSG00000069089
• Aliases: Cdk7, AI323415, AI528512, C230069N13, Cdkn7, Crk4
• Description: cyclin-dependent kinase 7 [Source:MGI Symbol;Acc:MGI:102956]

Sequence

>retro_mmus_383
ATGGCTGTGGACGTAAAATCTCAAGCGAAACGCTATGAAAAACTGGACTTCTTCGGACAGGGACATTTTGCTACAGCCTA
TAAGGCCAGAGATAAGAACACCAACCAAATCGTCACCATTAAGAAAATCAAACTTGGACACAGGTCAGAAGCTAAAGGTG
GTATAAATAGAACAGCCTTAAGGGAGATAAAGCTCTTACAGAAACTAAGTCATCCGAACACAATTGGTCTCCTTGACACA
TTTGGACATAAGTCTAACATTAGCCTTGTCTTGGATGTTATGGAAACTGACCTAGAGGTTATAATAAAGGATAACAGTCT
TGTGCTGACACCATCCCACATTCAAGCCTACATGTTGATGGCTTTTCAGGGCTTAGAATATTTGCATCAGCATTGGATTC
TACACAGGGATCTGAAACCAAAGGACTTCTTGTTAGATAAGAATGGAGTTCTGAAACTGGCAGACTTTGTCCTGGTCAAA
TCATTTGGGAGCCCCAGCAGGACTTACACACATCAAGTTGTGACCAGATGGTATTGGGCC

Alignment

ORF - retro_mmus_383 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 52.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTALREIKLLQELS
          MAVDVKS.AKRYEKLDF.G.G.FAT.YKARDKNTNQIV.IKKIKLGHRSEAK.GINRTALREIKLLQ.LS
Retrocopy MAVDVKSQAKRYEKLDFFGQGHFATAYKARDKNTNQIVTIKKIKLGHRSEAKGGINRTALREIKLLQKLS

Parental  HPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHWILHRDLKP
          HPN.IGLLD.FGHKSNISLV.D.METDLEVIIKDNSLVLTPSHI.AYMLM..QGLEYLHQHWILHRDLKP
Retrocopy HPNTIGLLDTFGHKSNISLVLDVMETDLEVIIKDNSLVLTPSHIQAYMLMAFQGLEYLHQHWILHRDLKP

Parental  NNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRWYRA
          ...LLD.NGVLKLADF.L.KSFGSP.R.YTHQVVTRWY.A
Retrocopy KDFLLDKNGVLKLADFVLVKSFGSPSRTYTHQVVTRWYWA

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	0.51 RPM	49.37 RPM
SRP007412_cerebellum	0.26 RPM	41.25 RPM
SRP007412_heart	0.06 RPM	22.66 RPM
SRP007412_kidney	0.29 RPM	28.20 RPM
SRP007412_liver	0.03 RPM	15.57 RPM
SRP007412_testis	0.46 RPM	16.24 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_383 was not detected

EST

No EST(s) were mapped for retro_mmus_383 retrocopy.

TSS

No TSS is located nearby retro_mmus_383 retrocopy 5' end.

Lab

retro_mmus_383 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_383 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
Homo sapiens	ENSG00000134058	1 retrocopy	retro_hsap_2335,
Gorilla gorilla	ENSGGOG00000013349	1 retrocopy	retro_ggor_1772,
Mus musculus	ENSMUSG00000069089	1 retrocopy	retro_mmus_383 ,
Otolemur garnettii	ENSOGAG00000010748	1 retrocopy	retro_ogar_986,
Procavia capensis	ENSPCAG00000002566	1 retrocopy	retro_pcap_318,
Pongo abelii	ENSPPYG00000015525	1 retrocopy	retro_pabe_2114,
Pan troglodytes	ENSPTRG00000016946	1 retrocopy	retro_ptro_1707,
Tupaia belangeri	ENSTBEG00000012193	2 retrocopies	retro_tbel_587, retro_tbel_637,