RetrogeneDB ID: retro_cpor_149

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_0:20969150..20969710(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OTX2
• Ensembl ID: ENSCPOG00000003420
• Aliases: None
• Description: None

Sequence

>retro_cpor_149
TCTTACCTTAAGCAACCGCCTCGTGCAGTCAATGGGCTGAGTTCACCACTTCGGGCATGGACTTGCTGCACCCCTCCATG
GGCTATCCAGCCACCCTATGGAAACGGTGGCAGGAGAGGACAGCCTTCATCCAGGGGTGAGATGTGCTGGAGGCGCTGTT
TGCCAAGACCCAATACCCAGACATGTTCATGCATGAGGAAGTGGCACTGAAAATCACCCTGCCTGGCCCCAGGGTGCAGG
TGTGGTTTGAGAACTGAAGAGCTAAGTGCCACCGGCAACAGTAGCAACAGCAGAATGGAGGTCAAAACAAAGTGAGATCT
ACCAAAAAGAAGACTTCTCCAGCGCGGGAAGTCAGTTCAGAGAGTGGAACGAGTGGCCAGTTCATTCCCTCCTCTAGCAC
CTCGGTCCGGACCATTGCCAGCAGCAGTGCTCACTCCCGTGTCTATCTGGAGCCCAGCCTCCATCTCCCCACTGTCAGAC
TTGTCCACCTCCTCCTCCTGCATGCAGAGGTCCTACCTATGGCCTACACTCAGGCTTCAGGTTATAGTCAAGGATATGCG

Alignment

ORF - retro_cpor_149 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.59 %
• Parental protein coverage: 72.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SYLKQPPYAVNGLS-LTTSGMDLLHPSVGYPATPRKQRRERTTFTRAQLDVLEALFAKTRYPDIFMREEV
          SYLKQPP.AVNGLS..TTSGMDLLHPS.GYPAT..K...ERT.F.....DVLEALFAKT.YPD.FM.EEV
Retrocopy SYLKQPPRAVNGLS<FTTSGMDLLHPSMGYPATLWKRWQERTAFIQG*-DVLEALFAKTQYPDMFMHEEV

Parental  ALKINLPESRVQVWFKNRRAKCHGGQ-NKVRPAKKKTSPAREVSSESGTSGQFTPSSSTSVPT-IASSSA
          ALKI.LP..RVQVWF.N.RAKCH..Q.........K........S...........S....P...A..S.
Retrocopy ALKITLPGPRVQVWFEN*RAKCHRQQ*QQQNGGQNKVRSTKKKTSPAREVSSESGTSGQFIPS>LAPRSG

Parental  PV--SIWSPASI-SPLS----DPLSTSSSCMQRSY-PMTYTQASGYSQGYA
          P.......P.SI.SP.S......LSTSSSCMQRSY.PM.YTQASGYSQGYA
Retrocopy PLPAAVLTPVSIWSPASISPLSDLSTSSSCMQRSY<PMAYTQASGYSQGYA

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	0.35 RPM	0.35 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP040447_lung	0.30 RPM	0.00 RPM
SRP040447_skeletal_muscle	0.01 RPM	0.00 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_149 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_149 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
Bos taurus	ENSBTAG00000014741	1 retrocopy	retro_btau_687,
Callithrix jacchus	ENSCJAG00000018583	1 retrocopy	retro_cjac_1380,
Cavia porcellus	ENSCPOG00000003420	1 retrocopy	retro_cpor_149 ,
Cavia porcellus	ENSCPOG00000012741	1 retrocopy	retro_cpor_1067,
Sus scrofa	ENSSSCG00000005063	1 retrocopy	retro_sscr_417,
Tursiops truncatus	ENSTTRG00000004650	1 retrocopy	retro_ttru_473,