RetrogeneDB ID: retro_cpor_1193

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_54:6437310..6438321(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADAL
• Ensembl ID: ENSCPOG00000002337
• Aliases: None
• Description: None

Sequence

>retro_cpor_1193
TATATTCTAATCAATCAAAATGAACTCTATGCCCCACCTGAATGGGTCCATTAGTTCAAATACCATGAAGAAATTAACAG
ACCAGAAGCCAGATTTTAGCATCAACCACCAGATGACTATGACTGACAAAGGAAAGAACTTTTGAAGAGTAAGTTTGAGA
AGACGTTTCCAGATGTTTCAAATTATTCATCAGTTTACTACTGACCTTGAAGCTATTCTAATGGTCACAAAAGATGTCAT
TTAAGAATTTGCTGGTGATGGTGTCAAGTAACAGGAACTGAGGAGCACACCCAGAAGAGAAAATGCTGCTAGAATGACTA
AAAAGACGTATGTGGAATCATACTTTTGGGTTTAAAACAGTCCAAACAAGGAAATTTAGACAGTGATGTTAGGTATTTGA
TAGCAGTTGACAGAAGAGGCGGCTAATTGGTAGCCAAAGAGACTATTAAACTCACTTAAGAGTTCTTCCTTTCAGCCGAG
GATACAGCTTTTGGCCTTGACCTCAGTGGAGATCCTACTATAGGACAAGTGAAAGACTTCTTGGAACCACTTTTAGAAGT
GAAAACAGCAGGCCTAAAGTTGGCATTGCTCCTTTCAGAGGTCCCAGATCAAAAAGAAGAAACCAAGATGTTCCTGGATC
TCCTTCCTGACAGAATCAGGCATAGAATATTTTCAACTCCTCTGAGAGAGGATCCCTGGCTCTGGTGAACTATGAGGCAG
CATCAGATCTCACTGGAAACCTGTTTGACTTCAAGCATCAAACATCAGATGGTTCCGTCTTGTGACCAGCATCACTTAAG
ATTCTGGTACAGCATTTCTCATCCATCTGTGATCTATACTGATGATAAGGGTGTTTTTCAAGAAATATGCCTTCCTCAAG
AGTACCAGCTAGCAGCAGAAACATTTAAATTGCCCAGTTCTCAGGTGTGGGATCTGTCTTATGAGTCCATCAACTACATT
TTTACTTCTGACAGCACCAGATCTGAATGGAGGAAGAAGAGCAATCATCTT

Alignment

ORF - retro_cpor_1193 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.18 %
• Parental protein coverage: 94.08 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YLELPKVELHA-HLNGSISSDTMKKLIAKKPDLNINSQMTVIDKGK---KRTLEECFQMFQIIHQLTTGP
          Y......EL.A.HLNGSISS.TMKKL...KPD..IN.QMT..DKGK......L...FQMFQIIHQ.TT..
Retrocopy YILINQNELYA>HLNGSISSNTMKKLTDQKPDFSINHQMTMTDKGKNF*RVSLRRRFQMFQIIHQFTTDL

Parental  EDILMVTKDVIKEFADDGVKYLELRSTPRRENATGMTKKTYVES-ILEGIKQSKQENLDIDVRYLIAIDR
          E.ILMVTKDVI.EFA.DGVK..ELRSTPRRENA..MTKKTYVES.IL.G.KQSKQ.NLD.DVRYLIA.DR
Retrocopy EAILMVTKDVI*EFAGDGVK*QELRSTPRRENAARMTKKTYVES<ILLGLKQSKQGNLDSDVRYLIAVDR

Parental  RGGSLVAKETVKLAEEFFLSANDTVLGLDLSGDPTIGQAKDFLEPLLEAKKTGLKLALHLSEVTNLVKET
          RGG.LVAKET.KL..EFFLSA.DT..GLDLSGDPTIGQ.KDFLEPLLE.K..GLKLAL.LSEV.....ET
Retrocopy RGG*LVAKETIKLT*EFFLSAEDTAFGLDLSGDPTIGQVKDFLEPLLEVKTAGLKLALLLSEVPDQKEET

Parental  QVLLDLLPDRIGHGTFLNSPERGSLDLVNFVRQHRIPLELCLTSNIKSQTVSSYDQHHFGFWYSISHPSV
          ...LDLLPDRI.H..F...P.R....L....RQH.I.LE.CLTS.IK.Q.V.S.DQHH..FWYSISHPSV
Retrocopy KMFLDLLPDRIRHRIF-STPLREDPWLW*TMRQHQISLETCLTSSIKHQMVPSCDQHHLRFWYSISHPSV

Parental  ICTDDKGVFAT-CLSQEYQLAAETFKLTKSQVWDLSYESINYIFASDSTRSKLRKKWNHL
          I.TDDKGVF...CL.QEYQLAAETFKL..SQVWDLSYESINYIF.SDSTRS..RKK.NHL
Retrocopy IYTDDKGVFQEICLPQEYQLAAETFKLPSSQVWDLSYESINYIFTSDSTRSEWRKKSNHL

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	9.20 RPM
SRP017611_kidney	0.00 RPM	9.74 RPM
SRP017611_liver	0.00 RPM	4.66 RPM
SRP040447_lung	0.00 RPM	7.31 RPM
SRP040447_skeletal_muscle	0.00 RPM	7.71 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1193 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1193 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014476	1 retrocopy	retro_btau_1539,
Cavia porcellus	ENSCPOG00000002337	1 retrocopy	retro_cpor_1193 ,
Oryctolagus cuniculus	ENSOCUG00000024818	2 retrocopies	retro_ocun_1237, retro_ocun_85,
Sus scrofa	ENSSSCG00000004710	1 retrocopy	retro_sscr_530,