RetrogeneDB ID: retro_cpor_861

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_3:54656460..54657661(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: API5
• Ensembl ID: ENSCPOG00000011993
• Aliases: None
• Description: None

Sequence

>retro_cpor_861
ATATTAACTCAACTTTTGCAGACAGAAGACTCTGCAGAATTTAACTTAGTGAACAATGCCCTGTTAAGTATATTTAAGAT
GGATGCAAAAGGAACTTTAGGTGGCTTGTTTAGCCAGATACTACAAGGAGAGGACATTGTTAGAGAATGAGCAATTAAAT
TCCTTTCTACAAAACTTAAGACTTTACCAGATGAAGTCTTAATGAAGGAAGTAGAAGAACTTATACTGACTGAATCCAAA
AAGGTCCTAGAAGATATGACTGGTGAAGAATTTGTTCTGTTCATGAAGATACTGTCTGGATTGAAAAGCTGACATACAGT
GAGTGGGAGACAGCAGTTGGCAGAGCTGGTGGCCGAGCAGGCTGACCTGGAGCAGACCTTCAATCCTTCAGACCCTGACT
GTGTGGACAGGCTCCTGCAGTGCACTTGACAGGTGGTACCCCTCTTCTCTAAAAATGTCCATTCTACAAGGTTTGTGACT
TATTTCTGTGAGCAAGTTCTCCCGAACCTCAGTACCTTGACTACCCCAGTGGAGGGTCTTGATATACAATTGGAGGTGTC
AAAATTGTTGGCAGAAATGAGTTCATTTTGTGGTGACATGGAGAAGCTAGAAACAAATTTAAGGAAACTATTTGATAAGT
TATTGGAGTACATGCCTCTTTCACCAGAAGAAGGAGAAAATGGGGAGAATGCTGGTAATGAAGAACCCAATTTGCAGTTC
AGTTATGTAGAATGGTTGTTACACAGTTTTCATCAGTTGGGCCGAAAACTCCCAGATTTCTTAACAGCCAAACTGAATGC
AGAAAAGCTCAAAGATTTCAAAATCAGGCTGCAGTACTTTGCCCGGGGCTTGAAGGTTTATGTCTGACAACTTGGCTTGG
CTCTCCAGGGTAAAAAAGGCGAGGCCTTAAAAACTGAAGAGAACAAGATTAAAGTTGTTGCATTGAAAATAACAAACAAT
ATCAATGTTTTAATCAAGGATCTCTTCCACATTCCTCCTTCTTATAAAAGCACAGTGACATTGTCTTGGAAACCTGTACA
GAAGGTTGAGATTGGGCAAAAGAGTTGTATCTTCATTAGATACAACTTCAAGTTCACCACCCAGGAAATCTCCAGCAGGA
CCAAAAAGAGATGCCAGGAAGATTTATAATCCCCACAGTGGGAAATGCAGCAGCAACTTGGGCAACTTTAATTATGAGCA
G

Alignment

ORF - retro_cpor_861 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.77 %
• Parental protein coverage: 79.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ILTQLLQTDDSAEFNLVNNALLSIFKMDAKGTLGGLFSQILQGEDIVRERAIKFLSTKLKTLPDEVLTKE
          ILTQLLQT.DSAEFNLVNNALLSIFKMDAKGTLGGLFSQILQGEDIVRE.AIKFLSTKLKTLPDEVL.KE
Retrocopy ILTQLLQTEDSAEFNLVNNALLSIFKMDAKGTLGGLFSQILQGEDIVRE*AIKFLSTKLKTLPDEVLMKE

Parental  VEELILTESKKVLEDVTGEEFVLFMKILSGLKSLQTVSGRQQLVELVAEQADLEQTFNPSDPDCVDRLLQ
          VEELILTESKKVLED.TGEEFVLFMKILSGLKS..TVSGRQQL.ELVAEQADLEQTFNPSDPDCVDRLLQ
Retrocopy VEELILTESKKVLEDMTGEEFVLFMKILSGLKS*HTVSGRQQLAELVAEQADLEQTFNPSDPDCVDRLLQ

Parental  CTRQAVPLFSKNVHSTRFVTYFCEQVLPNLSTLTTPVEGLDIQLEVLKLLAEMSSFCGDMEKLETNLRKL
          CT.Q.VPLFSKNVHSTRFVTYFCEQVLPNLSTLTTPVEGLDIQLEV.KLLAEMSSFCGDMEKLETNLRKL
Retrocopy CT*QVVPLFSKNVHSTRFVTYFCEQVLPNLSTLTTPVEGLDIQLEVSKLLAEMSSFCGDMEKLETNLRKL

Parental  FDKLLEYMPLPPEEAENGENAGNEEPKLQFSYVECLLYSFHQLGRKLPDFLTAKLNAEKLKDFKIRLQYF
          FDKLLEYMPL.PEE.ENGENAGNEEP.LQFSYVE.LL.SFHQLGRKLPDFLTAKLNAEKLKDFKIRLQYF
Retrocopy FDKLLEYMPLSPEEGENGENAGNEEPNLQFSYVEWLLHSFHQLGRKLPDFLTAKLNAEKLKDFKIRLQYF

Parental  ARGLQVYIRQLRLALQGKTGEALKTEENKIKVVALKITNNINVLIKDLFHIPPSYKSTVTLSWKPVQKVE
          ARGL.VY..QL.LALQGK.GEALKTEENKIKVVALKITNNINVLIKDLFHIPPSYKSTVTLSWKPVQKVE
Retrocopy ARGLKVYV*QLGLALQGKKGEALKTEENKIKVVALKITNNINVLIKDLFHIPPSYKSTVTLSWKPVQKVE

Parental  IGQKR-ANEDTTSGSPP-KKSAAGPKRDARQIYNPPSGKYSSNLGNFNYER
          IGQK.......T..S.P..KS.AGPKRDAR.IYNP.SGK.SSNLGNFNYE.
Retrocopy IGQKS>VSSLDTTSSSPPRKSPAGPKRDARKIYNPHSGKCSSNLGNFNYEQ

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	0.12 RPM	25.65 RPM
SRP017611_kidney	0.31 RPM	29.21 RPM
SRP017611_liver	0.09 RPM	28.12 RPM
SRP040447_lung	0.00 RPM	32.16 RPM
SRP040447_skeletal_muscle	0.03 RPM	15.96 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_861 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_861 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000011993	1 retrocopy	retro_cpor_861 ,
Myotis lucifugus	ENSMLUG00000013546	1 retrocopy	retro_mluc_245,
Macaca mulatta	ENSMMUG00000008827	1 retrocopy	retro_mmul_947,
Mus musculus	ENSMUSG00000027193	1 retrocopy	retro_mmus_2908,
Pongo abelii	ENSPPYG00000003345	1 retrocopy	retro_pabe_3805,
Vicugna pacos	ENSVPAG00000012428	1 retrocopy	retro_vpac_289,