RetrogeneDB ID: retro_mmus_1963

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:117240882..117241438(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081842
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rap1a
• Ensembl ID: ENSMUSG00000068798
• Aliases: Rap1a, AI848598, G-22K, Krev-1, Rap1
• Description: RAS-related protein-1a [Source:MGI Symbol;Acc:MGI:97852]

Sequence

>retro_mmus_1963
ATGTGTGAGTACAAGCTGGTGGTCCTTGGTTCAGGAGGCGTGGGGAAGTCTGCTCTGACAGTTCAGGTTTTTTTCCAGGG
AATTTTTGTTGAAAAATATGACTCAACAATAGATGATTCCTACAGAAAGCAAGTTGAAGTAGATTGCCAACAGTGTATGC
TGGAAATTCTGGACACCACAGGAACAGAGCAGTTTACAGTAATGAAGGATTTGTATATGAAGAATGGCCAAGGGTTTGCA
CTAGTTTACTCAATTACAGCTCAGTCTACATTTAATTGCTTACAAGACTTGAGAGAACAGATTTTACAGGTTAAAGACAC
AGCAGATGTTCCAATGATTTTGGTGGGCAATAAATGTGATCTGGAAGAATGTGCGGGTAGTTGGCAAAGAACAAGGCCAG
ACTTTAGCAAGACAGTGGTGTAACTGTGCCTTTTTAGAATCTTCTGCAAAGTCAAAGATCGATGTTAGTGAGATATTTTA
TGAGCTGGCCAGACAGATAAATAGAAAAACACCAGCGGGAAAGAAGAAGCCTAAAAAGAAATCACGCCTGCTGCTC

Alignment

ORF - retro_mmus_1963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.17 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MREYKLVVLGSGGVGKSALTVQ-FVQGIFVEKYDPTIEDSYRKQVEVDCQQCMLEILDTAGTEQFTAMRD
          M.EYKLVVLGSGGVGKSALTVQ.F.QGIFVEKYD.TI.DSYRKQVEVDCQQCMLEILDT.GTEQFT.M.D
Retrocopy MCEYKLVVLGSGGVGKSALTVQVFFQGIFVEKYDSTIDDSYRKQVEVDCQQCMLEILDTTGTEQFTVMKD

Parental  LYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLED-ERVVGKEQGQNLARQW
          LYMKNGQGFALVYSITAQSTFN.LQDLREQIL.VKDT.DVPMILVGNKCDLE...RVVGKEQGQ.LARQW
Retrocopy LYMKNGQGFALVYSITAQSTFNCLQDLREQILQVKDTADVPMILVGNKCDLEE>VRVVGKEQGQTLARQW

Parental  CNCAFLESSAKSKINVNEIFYDLVRQINRKTPVEKKKPKKKSCLLL
          CNCAFLESSAKSKI.V.EIFY.L.RQINRKTP..KKKPKKKS.LLL
Retrocopy CNCAFLESSAKSKIDVSEIFYELARQINRKTPAGKKKPKKKSRLLL

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	0.02 RPM	21.00 RPM
SRP007412_cerebellum	0.04 RPM	20.19 RPM
SRP007412_heart	0.00 RPM	30.07 RPM
SRP007412_kidney	0.00 RPM	33.59 RPM
SRP007412_liver	0.00 RPM	29.60 RPM
SRP007412_testis	0.00 RPM	7.96 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1963 was not detected

EST

No EST(s) were mapped for retro_mmus_1963 retrocopy.

TSS

No TSS is located nearby retro_mmus_1963 retrocopy 5' end.

Lab

retro_mmus_1963 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1963 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005384	1 retrocopy	retro_amel_1764,
Canis familiaris	ENSCAFG00000013686	1 retrocopy	retro_cfam_696,
Callithrix jacchus	ENSCJAG00000013392	7 retrocopies	retro_cjac_1671, retro_cjac_2218, retro_cjac_3376, retro_cjac_3707, retro_cjac_3843, retro_cjac_3844, retro_cjac_728,
Dasypus novemcinctus	ENSDNOG00000007809	5 retrocopies	retro_dnov_101, retro_dnov_1617, retro_dnov_1764, retro_dnov_628, retro_dnov_94,
Equus caballus	ENSECAG00000016434	1 retrocopy	retro_ecab_99,
Erinaceus europaeus	ENSEEUG00000010446	2 retrocopies	retro_eeur_306, retro_eeur_361,
Echinops telfairi	ENSETEG00000016893	2 retrocopies	retro_etel_1196, retro_etel_176,
Homo sapiens	ENSG00000116473	1 retrocopy	retro_hsap_1364,
Myotis lucifugus	ENSMLUG00000010571	3 retrocopies	retro_mluc_2311, retro_mluc_2312, retro_mluc_2313,
Monodelphis domestica	ENSMODG00000001323	3 retrocopies	retro_mdom_1327, retro_mdom_139, retro_mdom_1777,
Mus musculus	ENSMUSG00000052681	1 retrocopy	retro_mmus_1370,
Mus musculus	ENSMUSG00000068798	2 retrocopies	retro_mmus_1963 , retro_mmus_3027,
Nomascus leucogenys	ENSNLEG00000004018	1 retrocopy	retro_nleu_1069,
Ochotona princeps	ENSOPRG00000003999	3 retrocopies	retro_opri_321, retro_opri_460, retro_opri_875,
Pongo abelii	ENSPPYG00000001028	1 retrocopy	retro_pabe_1132,
Pan troglodytes	ENSPTRG00000001102	1 retrocopy	retro_ptro_937,
Rattus norvegicus	ENSRNOG00000032463	3 retrocopies	retro_rnor_1147, retro_rnor_1494, retro_rnor_1639,
Ictidomys tridecemlineatus	ENSSTOG00000027847	1 retrocopy	retro_itri_81,
Tarsius syrichta	ENSTSYG00000004521	3 retrocopies	retro_tsyr_1546, retro_tsyr_1829, retro_tsyr_2140,
Vicugna pacos	ENSVPAG00000010033	1 retrocopy	retro_vpac_491,