RetrogeneDB ID: retro_cpor_1476

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_9:39779987..39780795(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DTWD1
• Ensembl ID: ENSCPOG00000003461
• Aliases: None
• Description: None

Sequence

>retro_cpor_1476
GAAGATCTTCCTCAAAACTCCTTCTTAGAATCTCAAGAAATTCTTCAAAAAGCTCAGCATAGTGGGAGGTCAAAATGTGT
CAAGTGCAGTGGCTGAAGGATGTGTTGCTGCTATACCTGTTCTGTACCAGTAGAAAATGTAACCCTTGGACAGATTCCAC
TTGGGAAGCTGTCTCTGAAGACTGACATCATTAAACATCCAAATGTAACAGATGGCAAAAGCACTGCTGTCCTTGCAAAA
CTCTTAGCACCTGGATTTGTAAGCATTTACACATACCCTTATATTCTGCAATATGAAGCAAAGGACCTTGAAGTCACACT
TATTTTTCCTGGCCCTCAGTCTATCTCAATAAGATATTTCTTTTCATCTGCAAAAAAAAAAAGGATTCAAAATAAAGGCA
AAACTAATAACCTTGAGAGGCCACCTTTAAACACAAGAAACTAAAGAGGAGGAGAACTGTGATTTGAATGACGGAAGATG
CCCAGTTAGAACACTGAAAAGAGTGGTCTTTATGGACAGCACCTGGAACCAGACAAACACCACAGTCACTGAGAGCAGCT
GCAGGGGTTGTTACAAAGTTGAGTTAAAAACAAGAAAAATTTTCTTTTGGTGCCATCAAAAGGGAAAGTCAGATACTTTC
CTTTCCACAGTTGAAGCCATTTATTGTTTTCTAGTAGACTACTATGCTGACTTATTAAAAGAGAAACACAAAGGACAATA
TGACAATCTTCTATTTTTCTATTCTTTTATGTACCAGTTTATGAAAAATGCCAAATATTCTGGAGCTAAGCAAACAACAA
AACTCACA

Alignment

ORF - retro_cpor_1476 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.59 %
• Parental protein coverage: 89.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EDPLQNLCLASQEILQKAQRSGRSRCVKCGGSRMFYCYTCYVPVENVPGGQIPLVKLPLKIDIIKHPNET
          ED..QN..L.SQEILQKAQ.SGRS.CVKC.G.RM..CYTC.VPVENV..GQIPL.KL.LK.DIIKHPN.T
Retrocopy EDLPQNSFLESQEILQKAQHSGRSKCVKCSG*RMCCCYTCSVPVENVTLGQIPLGKLSLKTDIIKHPNVT

Parental  DGKSTAIHAKLLAPEFVNIYTYPCIPEYEEKDHEVALIFPGPQSVSIKDI-SFHLQKRIQNKGKTDDLER
          DGKSTA..AKLLAP.FV.IYTYP.I..YE.KD.EV.LIFPGPQS.SI....S......IQNKGKT..LER
Retrocopy DGKSTAVLAKLLAPGFVSIYTYPYILQYEAKDLEVTLIFPGPQSISIRYFFSSXXXXXIQNKGKTNNLER

Parental  P-SFKRKK-TEEQERCDLNDSKCKGATLKRVIFIDSTWNQTNKIVSDERLQGLLQVELKTRKTCFWRHQK
          P..FK.KK.T.E.E.CDLND..C...TLKRV.F.DSTWNQTN..V......G...VELKTRK..FW.HQK
Retrocopy P<TFKHKK<TKEEENCDLNDGRCPVRTLKRVVFMDSTWNQTNTTVTESSCRGCYKVELKTRKIFFWCHQK

Parental  GKPETFLSTIEAIYYFLVDYHTDILKEKYKGQYDNLLFFYSFMYQLIKNAKYSGTKQTTKLT
          GK..TFLST.EAIY.FLVDY..D.LKEK.KGQYDNLLFFYSFMYQ..KNAKYSG.KQTTKLT
Retrocopy GKSDTFLSTVEAIYCFLVDYYADLLKEKHKGQYDNLLFFYSFMYQFMKNAKYSGAKQTTKLT

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	6.10 RPM
SRP017611_kidney	0.00 RPM	10.57 RPM
SRP017611_liver	0.00 RPM	9.58 RPM
SRP040447_lung	0.00 RPM	7.62 RPM
SRP040447_skeletal_muscle	0.00 RPM	9.89 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1476 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1476 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014926	1 retrocopy	retro_cfam_2081,
Cavia porcellus	ENSCPOG00000003461	2 retrocopies	retro_cpor_1476 , retro_cpor_250,
Homo sapiens	ENSG00000104047	1 retrocopy	retro_hsap_2846,
Gorilla gorilla	ENSGGOG00000027921	1 retrocopy	retro_ggor_1973,
Nomascus leucogenys	ENSNLEG00000006167	1 retrocopy	retro_nleu_1598,
Otolemur garnettii	ENSOGAG00000013291	1 retrocopy	retro_ogar_499,
Ochotona princeps	ENSOPRG00000002951	2 retrocopies	retro_opri_136, retro_opri_949,
Pongo abelii	ENSPPYG00000006464	2 retrocopies	retro_pabe_2355, retro_pabe_2356,
Pan troglodytes	ENSPTRG00000007058	1 retrocopy	retro_ptro_1928,
Vicugna pacos	ENSVPAG00000008358	2 retrocopies	retro_vpac_509, retro_vpac_530,