RetrogeneDB ID: retro_cpor_1451

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_86:3378058..3379016(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABI1
• Ensembl ID: ENSCPOG00000014424
• Aliases: None
• Description: None

Sequence

>retro_cpor_1451
AATAACTAGCCTGCAAGAACTGGCACATAATTGAGCACAGATCCTCCTGCTAAGAAACCCCAAAGCCCTCCCATATCATG
CTGGGGAACACGGGGAAGAAGTCCTCTCACAAAATCCCTGCAGCCTGCTAAACCCCCAACCGTTCCTAATGATTGCATGT
CCAGTCCTGCAAGGCTCAGAAGTCAGCCTAGTCCAGGCAGGACAGCTTTTTAAATCAGAGAGCAAGGACATACAGTGGAA
GGAGTGGAGAAAGGGAAGTTGAGGGAACAGTGGGGTCAGTGGAACAGGCATCCCCCCTGCTGCACCCTCTCCCTCCCCAC
CCAGACCTGGACCAGGGCCCTCAGCTTGGCTCCTGGTTCCAATATGGCACCAGGACCAGGCAGATTTCTCCAAGCCACTC
TGCCATGTCCTCCAGAGCTTCTGGTGGGCACAGATGAATTCCCTCTGTGACTGCTCAGTTTTCTGCCAAGCTGCATGTTA
GTGGAGGTGCACTTTATTCTCAGAATTTAGTTTCTATTGTTACACCCCTCCTCCCATGCCTCTAGTGACTCCACACATAC
TTCACCCAGGCTTCATGGTCAGGGTGCAGGAAAACACTGTTGACAGCCCAGCTCCACCTCCACCAGATGTTGTTCCTGAA
TGTGATGACTGTTCACCTCCACCCCTGCCCCTCTCCCAGGAGACTATAAGATGAACAAGCCTGATTATTATTATTATAAT
CCCTATAATAATAATCCCTATGCAGATGGGGAGCCTGCCTGGGCCCCCAAGAATTATACTGAGAAAGTTGTTGCAATATA
TGATCATACAAAAGACAAGGCTCATGAGGTGTCATTTATGGAGGGTGCAATCACTGATGTTAGAAATAAGAACCACTATG
GTTGCCATGAAGCGATCGGCAGTCCAGTACTGGTCACTTCCTGGGAACTGCGTTGAGTCAGGCACGCACTATGCTGAT

Alignment

ORF - retro_cpor_1451 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.66 %
• Parental protein coverage: 66.53 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  NNQPARTGTLSRTNPPTQKPPSPPMSGRGTLGRNTPYKTLEPVKPPTVPNDYMTSPARLGSQHSPGRTA-
          NN.PARTGT...T.PP..KP.SPP.S..GT.GR....K.L.P.KPPTVPND.M.SPARL.SQ.SPGRTA.
Retrocopy NN*PARTGT*LSTDPPAKKPQSPPISCWGTRGRSPLTKSLQPAKPPTVPNDCMSSPARLRSQPSPGRTA<

Parental  SLNQRPRTHSGSSG-GSGSRENSGSSSIGIPIAVPTPSPPTIAPA-APGSAPGS-QYGTMTRQISRHNST
          .LNQR.RT.SG.SG...GS..NSG.S..GIP.A.P.PSPP...P..A...APGS.QYGT.TRQIS...S.
Retrocopy FLNQRARTYSGRSG<RKGS*GNSGVSGTGIPPAAPSPSPPRPGPG<ALSLAPGS<QYGTRTRQISPSHSA

Parental  TSSTSSGGYRRTPSVTAQFSAQPHVNGGPLYSQNSISIAPP-PPPMPQLTPQIPLTGFVARVQENIADSP
          .SS..SGG.R..PSVTAQFSA..HV.GG.LYSQN..SI..P.PPPMP..TP.I...GF..RVQEN..DSP
Retrocopy MSSRASGGHR*IPSVTAQFSAKLHVSGGALYSQNLVSIVTP<PPPMPLVTPHILHPGFMVRVQENTVDSP

Parental  TPPPPPPPDDIPIFDD-SPPP-PPPPPVDYEDEEAAVVQYN----DPYADGDPAWAPKNYIEKVVAIYDY
          .PPPP...D..P..DD.SPPP.P.P.P.DY.........YN.....PYADG.PAWAPKNY.EKVVAIYD.
Retrocopy APPPP---DVVPECDDCSPPP<PAPLPGDYKMNKPDYYYYNPYNNNPYADGEPAWAPKNYTEKVVAIYDH

Parental  TKDKDDELSFMEGAIIYVIKKNDDGWYEGVCNRV-TGLF-PGNYVESIMHYTD
          TKDK..E.SFMEGAI..V..KN..G..E.....V.TG.F.PGN.VES..HY.D
Retrocopy TKDKAHEVSFMEGAITDVRNKNHYGCHEAIGSPV<TGHF<PGNCVESGTHYAD

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	35.49 RPM
SRP017611_kidney	0.00 RPM	30.25 RPM
SRP017611_liver	0.00 RPM	23.85 RPM
SRP040447_lung	0.00 RPM	47.16 RPM
SRP040447_skeletal_muscle	0.00 RPM	8.59 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1451 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1451 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 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014424	3 retrocopies	retro_cpor_1274, retro_cpor_1375, retro_cpor_1451 ,