RetrogeneDB ID: retro_rnor_476

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:127744709..127745281(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000011510
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Cwc15
• Ensembl ID: ENSRNOG00000008490
• Aliases: Cwc15, RGD1310669
• Description: Spliceosome-associated protein CWC15 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q5BJP2]

Sequence

>retro_rnor_476
CATACAAAGATAAAGTACAGACAAACCACACAGGATGGCCCTGAAGAGGTTTGCAACTGTGACTTCAGGAGAGAGTTGGA
AGAGAGGGAGAGAGCTGCTGCAAGGGAGAAAAATAGGGACCGTCCAACCCGAAAACACACAACTTCCTCCTCAGTGTCCA
AGAAGCCCCGCTTAGACCAGATCCCTGCTGCCAACCTTGACGCTGACGATCCTCTCACAGATGAGGAAGATGAGGATTTT
GAAGCGGAGAGTGATGACGATGATACTGCAGCTCTTCTAGCAGAGCTAGAAAAGATCAAGAAGGAGAGAGCTGAAGAGCA
GGCCAGGAAGGAACAAGAACAAAAAGCAGAGGAAGAGAGAATTCGCATGGAAAACATTCTGAGTGGAAACTTCCTGAATC
TCACTGGCCCATCCCAGCCTCAGGCCAACTTCAAGGTTAAAAGAAGGTGGGACGATGGTGTTATTTTTAAGAACTGTGCA
AAGGAGATAGATGATCAAAAGACAGACAAAAATTTGTAAACGATGCACTGCAATCTGAATTTCACAAAAAGTTCATGAAG
AAATATATTAAG

Alignment

ORF - retro_rnor_476 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.71 %
• Parental protein coverage: 83.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HTKIKYRQTTQDAPEEVRNRDFRRELEERERAAAREKNRDRPTREHTTSSSVSKKPRLDQIPAANLDADD
          HTKIKYRQTTQD.PEEV.N.DFRRELEERERAAAREKNRDRPTR.HTTSSSVSKKPRLDQIPAANLDADD
Retrocopy HTKIKYRQTTQDGPEEVCNCDFRRELEERERAAAREKNRDRPTRKHTTSSSVSKKPRLDQIPAANLDADD

Parental  PLTDEEDEDFEEESDDDDTAALLAELEKIKKERAEEQARKEQEQKAEEERIRMENILSGNPLLNLTGPSQ
          PLTDEEDEDFE.ESDDDDTAALLAELEKIKKERAEEQARKEQEQKAEEERIRMENILSGN..LNLTGPSQ
Retrocopy PLTDEEDEDFEAESDDDDTAALLAELEKIKKERAEEQARKEQEQKAEEERIRMENILSGN-FLNLTGPSQ

Parental  PQANFKVKRRWDDDVVFKNCAKGIDDQKKDK-RFVNDTLRSEFHKKFMEKYIK
          PQANFKVKRRWDD.V.FKNCAK.IDDQK.DK..FVND.L.SEFHKKFM.KYIK
Retrocopy PQANFKVKRRWDDGVIFKNCAKEIDDQKTDK<KFVNDALQSEFHKKFMKKYIK

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	27.39 RPM
SRP017611_kidney	0.00 RPM	29.66 RPM
SRP017611_liver	0.00 RPM	16.47 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_476 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_476 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_476 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011392	1 retrocopy	retro_amel_1913,
Bos taurus	ENSBTAG00000007913	1 retrocopy	retro_btau_703,
Canis familiaris	ENSCAFG00000004134	6 retrocopies	retro_cfam_1329, retro_cfam_2123, retro_cfam_503, retro_cfam_537, retro_cfam_61, retro_cfam_805,
Callithrix jacchus	ENSCJAG00000004188	1 retrocopy	retro_cjac_2802,
Cavia porcellus	ENSCPOG00000006249	1 retrocopy	retro_cpor_708,
Dipodomys ordii	ENSDORG00000011075	1 retrocopy	retro_dord_313,
Echinops telfairi	ENSETEG00000006649	1 retrocopy	retro_etel_647,
Felis catus	ENSFCAG00000007826	1 retrocopy	retro_fcat_1416,
Myotis lucifugus	ENSMLUG00000002032	3 retrocopies	retro_mluc_102, retro_mluc_2143, retro_mluc_2478,
Mus musculus	ENSMUSG00000004096	2 retrocopies	retro_mmus_2482, retro_mmus_593,
Ornithorhynchus anatinus	ENSOANG00000010404	1 retrocopy	retro_oana_5,
Oryctolagus cuniculus	ENSOCUG00000001629	4 retrocopies	retro_ocun_1037, retro_ocun_1605, retro_ocun_679, retro_ocun_743,
Otolemur garnettii	ENSOGAG00000001686	2 retrocopies	retro_ogar_2476, retro_ogar_456,
Rattus norvegicus	ENSRNOG00000008490	3 retrocopies	retro_rnor_2452, retro_rnor_251, retro_rnor_476 ,
Sarcophilus harrisii	ENSSHAG00000016534	5 retrocopies	retro_shar_26, retro_shar_333, retro_shar_447, retro_shar_596, retro_shar_768,
Tarsius syrichta	ENSTSYG00000000407	1 retrocopy	retro_tsyr_1585,