RetrogeneDB ID: retro_cpor_708

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_24:21714709..21715169(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CWC15
• Ensembl ID: ENSCPOG00000006249
• Aliases: None
• Description: CWC15 spliceosome-associated protein homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26939]

Sequence

>retro_cpor_708
GCTGCTAGAGAAAATAAAAATAAAGATTTTCCAACCCATGAACACATGATCTCTGCTCAGTGTCAAAAAAGCTTCCGTCA
CACCAGATTCCTACTGCAGCAGATCCTAGAACAGGGAAGGGGAGATGAAAACTTTGAAGTAGAGTGTGATGAGCCTGATA
TGCAGCTATTCTTGCAAAATTGCAAAGAATTAGAAAGAAGAGCTGGAGAACAGGCCAGGAAGGGACAAGGACCAACGCAG
AAAAGAAAGCATTGGTATAAAAAACATTCTAGGTAGAAACGCCCTCCTTCATCTCACCAGCCCACCGCAGCCTCTGGGGC
AGCTTCCCAGTGAAAAGAAGACAGGACAAGGATGTTGTCTTCAAGAACTGTGCCTACGGTGTAGAAGATCCAAAGAAATA
TGAAAGATTTGTAAATGTACACTGTGGTCTGAACTTCATAAAATGTTTGTGAAGAAACAT

Alignment

ORF - retro_cpor_708 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.3 %
• Parental protein coverage: 69.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  AAAREKNRDRPTREHTTSS-SVSKKPRLDQIPAANLDADDPLTDEE-DEDFEEESDDDDT-AALLAELEK
          AA...KN.D.PT.EH..S..SVSKK....QIP.....A.DP.T....DE.FE.E.D..D..AA.LA.L..
Retrocopy AARENKNKDFPTHEHMISA<SVSKKLPSHQIPT----AADPRTGKG>DENFEVECDEPDM<AAILAKLQR

Parental  IK-KERAEEQARKEQEQKAEEERIRMENILSGNPLLNLTGPSQPQA-NFKVKRRWDDDVVFKNCAKGVDD
          I..KE..E........Q...E..I...NIL..N.LL.LT.P.QP....F.VKRR.D.DVVFKNCA.GV.D
Retrocopy IR<KEELENRPGRDKDQRRKES-IGIKNILGRNALLHLTSPPQPLG>SFPVKRRQDKDVVFKNCAYGVED

Parental  QKKDKRFVN-DTLRSEFHKKFMEKY
          .KK..RFVN..TL.SE.HK.F..K.
Retrocopy PKKYERFVN<CTLWSELHKMFVKKH

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	28.87 RPM
SRP017611_kidney	0.00 RPM	35.80 RPM
SRP017611_liver	0.00 RPM	27.51 RPM
SRP040447_lung	0.00 RPM	21.54 RPM
SRP040447_skeletal_muscle	0.00 RPM	23.22 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_708 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_708 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
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 ,
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,
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,