RetrogeneDB ID: retro_cpor_637

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_20:34031174..34031725(-)
• Located in intron of: ENSCPOG00000024727

Retrocopy information

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

Parental gene information

• Parental gene symbol: DAZL
• Ensembl ID: ENSCPOG00000007628
• Aliases: None
• Description: None

Sequence

>retro_cpor_637
AGGAAACAAAATTTATATACTTATCATGTTCATCGACATCCTTTGATTTTTAATTCTCCACCAGCACAGTTTCGGAGTAT
TTGGGCCAATCCAAACACTGAAACTGATGCGCAGCCTCCAACCGTGATGAGTCCTATAATTCAGTATGTTCAGACATACC
CTCCATATCCATATTCACCAGTTCAGCTCATCGCTGGTTATCAGTGCCTGTTTATGATCATCAGATGCCACCACAATGGC
CTGCTGGGGAACAAAGGAGTCACGTTATACCTCTAGCTTATACAATGGTTAACTACCACTATAATGCCTTTGATCAAGGA
GCTGCAGTTTTGCCAAATGAATGCTCAGTTCATGAAGCTGCTTCATGCTCTGGAAATGGCCCATTAAAGAAATATGTGGA
CTGAAGCATTCAAGCAGTGGTATCTTAGTCTGTTTAACCCAGAGCATAGACTGAGAAACACTCTTGTTACTCAAGACGAG
TACTTCAAAGATTTTAAAAGAGTGCATCACTTAGAAGACATCACATAGTGCTTAAATCTGATCATCTCTGC

Alignment

ORF - retro_cpor_637 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.74 %
• Parental protein coverage: 62.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RKQNLCEGAYHVQPRPLIFNPPPPPQFQSVWSNPNTETYVQPPTMMSPITQYVQTYPPYPNSPVQVITGY
          RKQNL....YHV...PLIFN.PP..QF.S.W.NPNTET..QPPT.MSPI.QYVQTYPPYP.SPVQ.I.GY
Retrocopy RKQNLY--TYHVHRHPLIFNSPPA-QFRSIWANPNTETDAQPPTVMSPIIQYVQTYPPYPYSPVQLIAGY

Parental  Q-LPVYNYQMPPQWPAGEQRSYVIPPAYTTVNYHYNEVDPGAEVLPNECSVHEATSSSGNGPQKKSVDRS
          Q..PVY..QMPPQWPAGEQRS.VIP.AYT.VNYHYN..D.GA.VLPNECSVHEA.S.SGNGP.KK.VD.S
Retrocopy Q<VPVYDHQMPPQWPAGEQRSHVIPLAYTMVNYHYNAFDQGAAVLPNECSVHEAASCSGNGPLKKYVD*S

Parental  IQTVVS-CLFNPENRLRNTLVTQDDYFKD-KRVHH-FRRSRTVLKSEHLC
          IQ.VVS..LFNPE.RLRNTLVTQD.YFKD.KRVHH..RR...VLKS.HLC
Retrocopy IQAVVS>SLFNPEHRLRNTLVTQDEYFKDFKRVHH<LRRHHIVLKSDHLC

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	0.00 RPM
SRP017611_kidney	0.10 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP040447_lung	0.00 RPM	0.00 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.00 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_637 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_637 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	ENSBTAG00000000502	1 retrocopy	retro_btau_644,
Cavia porcellus	ENSCPOG00000007628	1 retrocopy	retro_cpor_637 ,
Otolemur garnettii	ENSOGAG00000006983	1 retrocopy	retro_ogar_1070,
Pteropus vampyrus	ENSPVAG00000007836	2 retrocopies	retro_pvam_1185, retro_pvam_674,