RetrogeneDB ID: retro_rnor_1891

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:71542742..71543447(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Paics
• Ensembl ID: ENSRNOG00000002101
• Aliases: Paics, Ade2h1, Airc
• Description: Multifunctional protein ADE2 Phosphoribosylaminoimidazole-succinocarboxamide synthase Phosphoribosylaminoimidazole carboxylase [Source:UniProtKB/Swiss-Prot;Acc:P51583]

Sequence

>retro_rnor_1891
ATATCAGGAAAAAACTCTGAGGGTAAAACAAAAGAAGTCTATGAATTGTTAGATAATCCAGGAAGAGTCCTCCTGCAGTC
CAAGGACCAGATTTCAACAGGAAATGCAGCTGGAAAAAAACACCCCCTGGAAGGCAAAGCTGCCATCTCCACTAAGGTCA
CCAGCTACATACTCCAGTTGTTTCAGGAAGCAACAATGTCTTTCACCACGAAATTTGGGGAGACTGCTTTCATTGCACCC
CAATGTGAAATGATTACAATTGAATGGGTGTGCTGAAGAGTAGCAACTGGATCTTTTCTCAAAAGTAACCCTGGTGTAAA
GGAGGGATTTAAGTTTTAACCACCAAAAGTAAAGACGTTCCTCAAGGATGATGCCAGTAATGACCCACAGTGGTCTGAGG
AGCAATTCATTGCTGCAAAACATTGTTTTGCTGGACTGGTTATAGGACAGACTGAAGTGGACATCATAAGTCATGCCACA
TAAGCTAATTTTGAAATTCTGGAGAAATCCTGGCTGCCCCAGAACTGTACTCTGATTGATAAGAAGATTGAATTTGGCAT
TGATGTAACCACCAAAGAGATTGTTTTTGCTGATGTCATAGATAATGAGTCCTGGACACCGTGGCCATCAGGAGATCGGA
GCCAGCAGAAAGACATAGTCTTACCGGGATCTAGAAGAAGTAACTCCAGAAGGACTCCAGATGGG

Alignment

ORF - retro_rnor_1891 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.95 %
• Parental protein coverage: 54.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IGRKLYEGKTKEVYELLDSPGRVLLQSKDQITAGNAARKNH-LEGKAAISNKITSCIFQLLQEAGIKTAF
          I..K..EGKTKEVYELLD.PGRVLLQSKDQI..GNAA.K.H.LEGKAAIS.K.TS.I.QL.QEA.....F
Retrocopy ISGKNSEGKTKEVYELLDNPGRVLLQSKDQISTGNAAGKKHPLEGKAAISTKVTSYILQLFQEATM--SF

Parental  TKKCGETAFIAPQCEMIPIEWVCRRIATGSFLKRNPGVKEGYRFYPPKVEMFFKDDANNDPQWSEEQLIA
          T.K.GETAFIAPQCEMI.IEWVC.R.ATGSFLK.NPGVKEG..F.PPKV..F.KDDA.NDPQWSEEQ.IA
Retrocopy TTKFGETAFIAPQCEMITIEWVC*RVATGSFLKSNPGVKEGFKF*PPKVKTFLKDDASNDPQWSEEQFIA

Parental  AKFCFAGLVIGQTEVDIMSHATQAIFEILEKSWLPQNCTLVDMKIEFGVDVTTKEIVLADVIDNDSWRLW
          AK.CFAGLVIGQTEVDI.SHAT.A.FEILEKSWLPQNCTL.D.KIEFG.DVTTKEIV.ADVIDN.SW..W
Retrocopy AKHCFAGLVIGQTEVDIISHAT*ANFEILEKSWLPQNCTLIDKKIEFGIDVTTKEIVFADVIDNESWTPW

Parental  PSGDRSQQKD---KQSYRDLKEVTPEG
          PSGDRSQQKD.....S.R.....TP.G
Retrocopy PSGDRSQQKDIVLPGSRRSNSRRTPDG

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
SRP017611_brain	0.00 RPM	10.93 RPM
SRP017611_kidney	0.00 RPM	30.43 RPM
SRP017611_liver	0.00 RPM	16.54 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1891 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1891 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1891 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,