RetrogeneDB ID: retro_mmus_1645

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:53702322..53702972(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rab5a
• Ensembl ID: ENSMUSG00000017831
• Aliases: Rab5a, 2410015H04Rik, AI663973, AU021172, nnyRab5a
• Description: RAB5A, member RAS oncogene family [Source:MGI Symbol;Acc:MGI:105926]

Sequence

>retro_mmus_1645
ATGGCTAATCTAGGAGCAACAAGAACCAACGGGCCAAATACTGGAAATAAAATATGCCAGGTCAAACTGGTCCTTCTAGG
AGAGTCTACTGTTGGCAAATAAAGCCTGGTGCTTCGCTTTGTGAAAGACCAATTTTATGAATTTCAAGAGAGTACCTCTG
GGGCTGCCTTTCTAACCCAAACTGTGGGTCTTGATGACACAACAGTAAAATTTGAAATATGGGATACAGCCGGGCAAGAA
CAGTATCATAGCCTAGCACCAATGTACTACCGAGAAGGACAAGCAGCCAGAGCTGTGTATGATATCGCGAATGTAGAATC
CATTTCGAGAGCAAAAAACTGGGTTTAAGAACTTCAAAGGCAAGCAAGTCCTAATATTGTGATAGTTTTAGAATAGCTAA
GAAACAAAGTTGACTTAGCAAATAAAACAGCCATTGGCTTCCAGGAAGCACAGTCCTATGCAGGTGACAACAGCTCACTA
TTTATGGAGACGGCAGCTAAGACATCAATGAATGTAAATGAAATATTTATGCAATAGCTAAAAAGCTGCCAAAAAATGAA
CCACAGAATCCTGGTGCAAACTCGGCCAGAGGACAAGGAGTAGACCTTACTGAGCCTGCACAGCCAGCCAGAAGCCAGTG
TTGTAGTAAC

Alignment

ORF - retro_mmus_1645 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MANRGATRPNGPNTGNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVK
          MAN.GATR.NGPNTGNKICQ.KLVLLGES.VGK.SLVLRFVK.QF.EFQEST.GAAFLTQTV.LDDTTVK
Retrocopy MANLGATRTNGPNTGNKICQVKLVLLGESTVGK*SLVLRFVKDQFYEFQESTSGAAFLTQTVGLDDTTVK

Parental  FEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALS--GNKADLA
          FEIWDTAGQE.YHSLAPMYYR..QAA..VYDI.N.ES..RAKNWV.ELQRQASPNIVI.L....NK.DLA
Retrocopy FEIWDTAGQEQYHSLAPMYYREGQAARAVYDIANVESISRAKNWV*ELQRQASPNIVIVLE*LRNKVDLA

Parental  NKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFM-AIAKKLPKNEPQNPGANSARGRGVDLTEPAQP
          NK.A..FQEAQSYA.DNS.LFMET.AKTSMNVNEIFM.AIAKKLPKNEPQNPGANSARG.GVDLTEPAQP
Retrocopy NKTAIGFQEAQSYAGDNSSLFMETAAKTSMNVNEIFM<AIAKKLPKNEPQNPGANSARGQGVDLTEPAQP

Parental  ARSQCCSN
          ARSQCCSN
Retrocopy ARSQCCSN

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	0.12 RPM	60.86 RPM
SRP007412_cerebellum	0.00 RPM	52.02 RPM
SRP007412_heart	0.00 RPM	24.16 RPM
SRP007412_kidney	0.00 RPM	34.30 RPM
SRP007412_liver	0.00 RPM	23.32 RPM
SRP007412_testis	0.00 RPM	9.33 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1645 was not detected

EST

No EST(s) were mapped for retro_mmus_1645 retrocopy.

TSS

No TSS is located nearby retro_mmus_1645 retrocopy 5' end.

Lab

retro_mmus_1645 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1645 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000954	1 retrocopy	retro_amel_958,
Bos taurus	ENSBTAG00000046385	1 retrocopy	retro_btau_300,
Callithrix jacchus	ENSCJAG00000003731	1 retrocopy	retro_cjac_3268,
Cavia porcellus	ENSCPOG00000005322	2 retrocopies	retro_cpor_1213, retro_cpor_219,
Dipodomys ordii	ENSDORG00000012429	1 retrocopy	retro_dord_288,
Felis catus	ENSFCAG00000004455	2 retrocopies	retro_fcat_1349, retro_fcat_984,
Homo sapiens	ENSG00000144566	1 retrocopy	retro_hsap_1074,
Gorilla gorilla	ENSGGOG00000015981	1 retrocopy	retro_ggor_848,
Loxodonta africana	ENSLAFG00000008321	1 retrocopy	retro_lafr_267,
Macaca mulatta	ENSMMUG00000006992	2 retrocopies	retro_mmul_227, retro_mmul_839,
Monodelphis domestica	ENSMODG00000014793	2 retrocopies	retro_mdom_1219, retro_mdom_1993,
Mus musculus	ENSMUSG00000000711	1 retrocopy	retro_mmus_2081,
Mus musculus	ENSMUSG00000017831	1 retrocopy	retro_mmus_1645 ,
Nomascus leucogenys	ENSNLEG00000003434	1 retrocopy	retro_nleu_2466,
Oryctolagus cuniculus	ENSOCUG00000012200	1 retrocopy	retro_ocun_1034,
Pongo abelii	ENSPPYG00000014074	2 retrocopies	retro_pabe_3094, retro_pabe_894,
Pan troglodytes	ENSPTRG00000014682	1 retrocopy	retro_ptro_731,
Ictidomys tridecemlineatus	ENSSTOG00000026229	1 retrocopy	retro_itri_398,
Tarsius syrichta	ENSTSYG00000007642	3 retrocopies	retro_tsyr_1544, retro_tsyr_315, retro_tsyr_946,
Tursiops truncatus	ENSTTRG00000001374	1 retrocopy	retro_ttru_949,