RetrogeneDB ID: retro_mmus_3126

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:40855230..40855958(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Paics
• Ensembl ID: ENSMUSG00000029247
• Aliases: Paics, 2610511I09Rik, ADE2H1, AIRC, PAIS
• Description: phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoribosylaminoimidazole, succinocarboxamide synthetase [Source:MGI Symbol;Acc:MGI:1914304]

Sequence

>retro_mmus_3126
ATTGCAGCAGGGAATGAAGCTAGAAAGAACCACCTGGAAGGCCAAGCTGCCGTCGCCAATAAGATCACCAGCTGCATATT
TCAGTTGTGACAGGAAGCTGGTATAAAAACTGCTTTCACCAAGAAATTTGGGGAGACTGCTTTCATTGCACCCCGATGTG
AAATGATTCCATTGAATAGGTATGGCAAAGACTAGCAACTGGATCTTTTCTCAAAAGGAACCCTGGGGTAAAGGAGGCGT
GTAAGTTTTATCTACCAAAAGTGGAGACGTTCTTCAAGGATGATGCCAGTAATGATGCACAGTGGCCTGAGGAGCAGCTC
ATCGCTGCAGAATTGTGCTTTGTTGGCCTTGTTATAGGGCAGACTGAAGTGGACATCATGAGTCATGCCACACAAGCTAT
TTTTGAAATTCTGGAGAAATCCTGGCTGCCCCAGGACTGTATGCTGGTTGATATGAAGATTGAACTTGGCATTGATGTAA
CCACCAAAGAGATTGTCCTTGCTGATGCCATTGATAATGGTTCCTGGAGACTATGGCCATCGGGAGATCGGAGCCAGCAG
AAAGACAAACAGTCTTACCATGATCTCAAAGAAGTAACTCCGGAAGGACTCCAGATGGTAAAGAAAGACTCTGAGTGGGT
TGCAGATCGAGTGGAGTTGCTTCTCAAGTCAGTCACTCAGTGCAGGGTGGTAGTGCTGATGGGCTCCACCTCTGACCTTG
GTCACTGT

Alignment

ORF - retro_mmus_3126 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.07 %
• Parental protein coverage: 57.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ITAGNAARKNHLEGKAAISNKITSCIFQLLQEAGIKTAFTKKCGETAFIAPQCEMIP-IEWVCRRIATGS
          I.AGN.ARKNHLEG.AA..NKITSCIFQL.QEAGIKTAFTKK.GETAFIAP.CEMIP.IE.V..R.ATGS
Retrocopy IAAGNEARKNHLEGQAAVANKITSCIFQL*QEAGIKTAFTKKFGETAFIAPRCEMIP<IE*VWQRLATGS

Parental  FLKRNPGVQEGYKFYPPKVEMFFKDDANNDPQWSEEQLIAAKFCFAGLVIGQTEVDIMSHATQAIFEILE
          FLKRNPGV.E..KFY.PKVE.FFKDDA.ND.QW.EEQLIAA..CF.GLVIGQTEVDIMSHATQAIFEILE
Retrocopy FLKRNPGVKEACKFYLPKVETFFKDDASNDAQWPEEQLIAAELCFVGLVIGQTEVDIMSHATQAIFEILE

Parental  KSWLPQDCTLVDMKIEFGVDVTTKEIVLADVIDNDSWRLWPSGDRSQQKDKQSYRDLKEVTPEGLQMVKK
          KSWLPQDC.LVDMKIE.G.DVTTKEIVLAD.IDN.SWRLWPSGDRSQQKDKQSY.DLKEVTPEGLQMVKK
Retrocopy KSWLPQDCMLVDMKIELGIDVTTKEIVLADAIDNGSWRLWPSGDRSQQKDKQSYHDLKEVTPEGLQMVKK

Parental  NFEWVADRVELLLKSDSQCRVVVLMGSTSDLGHC
          ..EWVADRVELLLKS..QCRVVVLMGSTSDLGHC
Retrocopy DSEWVADRVELLLKSVTQCRVVVLMGSTSDLGHC

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	0.23 RPM	72.47 RPM
SRP007412_cerebellum	0.09 RPM	76.99 RPM
SRP007412_heart	0.06 RPM	100.89 RPM
SRP007412_kidney	0.04 RPM	159.50 RPM
SRP007412_liver	1.07 RPM	189.96 RPM
SRP007412_testis	0.05 RPM	40.07 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3126 was not detected

EST

No EST(s) were mapped for retro_mmus_3126 retrocopy.

TSS

No TSS is located nearby retro_mmus_3126 retrocopy 5' end.

Lab

retro_mmus_3126 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3126 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010577	1 retrocopy	retro_btau_508,
Cavia porcellus	ENSCPOG00000010749	1 retrocopy	retro_cpor_969,
Dasypus novemcinctus	ENSDNOG00000013413	1 retrocopy	retro_dnov_284,
Echinops telfairi	ENSETEG00000015242	2 retrocopies	retro_etel_1918, retro_etel_341,
Homo sapiens	ENSG00000128050	3 retrocopies	retro_hsap_3802, retro_hsap_3915, retro_hsap_3927,
Gorilla gorilla	ENSGGOG00000024392	1 retrocopy	retro_ggor_2643,
Mus musculus	ENSMUSG00000029247	6 retrocopies	retro_mmus_1748, retro_mmus_2750, retro_mmus_2858, retro_mmus_3126 , retro_mmus_653, retro_mmus_971,
Nomascus leucogenys	ENSNLEG00000008786	2 retrocopies	retro_nleu_1274, retro_nleu_2156,
Otolemur garnettii	ENSOGAG00000003575	2 retrocopies	retro_ogar_2138, retro_ogar_865,
Procavia capensis	ENSPCAG00000008531	1 retrocopy	retro_pcap_172,
Pan troglodytes	ENSPTRG00000016081	2 retrocopies	retro_ptro_2662, retro_ptro_2670,
Rattus norvegicus	ENSRNOG00000002101	3 retrocopies	retro_rnor_1891, retro_rnor_2768, retro_rnor_804,
Tupaia belangeri	ENSTBEG00000006751	1 retrocopy	retro_tbel_3697,
Tarsius syrichta	ENSTSYG00000010497	2 retrocopies	retro_tsyr_2170, retro_tsyr_329,
Drosophila melanogaster	FBgn0020513	1 retrocopy	retro_dmel_82,