RetrogeneDB ID: retro_cpor_1464

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_89:6438130..6439010(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF207
• Ensembl ID: ENSCPOG00000001728
• Aliases: None
• Description: None

Sequence

>retro_cpor_1464
TACACCCAGTCATTTTGCAGCACAAACATAATGATGCCAATGGGTGGAATGATGCCACGTGGACCAGGACTACCACCTGT
CATGCCTTGTATGCCACCAGGCATGGTACCCCGTCCTGACGTCCTGGAATTCCTCCAATGACTCAAGCTCAGGCTGTTTC
AGCACCAGGAATTCTTAATAGACCTGGACCACCTGCACCAATTGCGACAGTGCTTGCCCCACAGCCTCTAGGTACTAAGC
CCCTTTTGCCCAGAGAGATGGGGACACCTGTAACAAGCTCAAGTACAGCTTCATCTAATTCAGAAAGTCTCTGCATCTTC
TAAAGCTCTGTTTCCTAGCACAGCAGAAGCTCAAGCAGCTGTTCAAGGATCTGTTGGTACAGATTTCAAGCCCATAAATA
GTATTCCTGCCATAACTACAGAACCTGCCAAACCTACATTCCCTGCTTATACACAGTCTACGGTTTCAATCACTAATACT
ACAAATAGTACTGCCACAAAAGCAGCACTTCAGTAACAAGTAAACCTGCTACACTTAAAACTAGCAGTGCAATAAGTAAG
TTGATCTATCCAGATGAGGATACATCACTGGAAGAGAGAAGGGCACAGTTATCTAAACACCAAAGTAATCTTCCTTGACC
AGGACAGGCCTCCATCACTAATCCAGCAGTTGTGTTTATTGGAAGTATGATGCCACCATAGCAGCAGGGCATGAGGCCTC
CAATGCCACCTCTTGGTCAGTATGGTAGTCATCATCAAGGCATGCCAGGTTATCTTCCTAGTGCAATGCCACCACATGTG
CAGGACCGCCGATGGTGCCCCCTAACTGCGACAGGACTCCTCGGCGTCCAGTGGGAATGAGATCTCCTGTAGTGTTGCAA

Alignment

ORF - retro_cpor_1464 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.2 %
• Parental protein coverage: 60.73 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YTQSFCGENIMMPMGGMMPPGPGIPPLMPGMPPGMPP-PVPRPGIPPMTQAQAVSAPGILNRP--PAPTA
          YTQSFC..NIMMPMGGMMP.GPG.PP.MP.MPPGM.P.P..RPGIPPMTQAQAVSAPGILNRP..PAP.A
Retrocopy YTQSFCSTNIMMPMGGMMPRGPGLPPVMPCMPPGMVP<PS*RPGIPPMTQAQAVSAPGILNRPGPPAPIA

Parental  TVPAPQPPVTKPLFPSAGQMGTPVTSSSTASSNS-ESLSASSKALFPSTAQAQAAVQGPVGTDFKPLNST
          TV.APQP..TKPL.P....MGTPVTSS....S......SASSKALFPSTA.AQAAVQG.VGTDFKP.NS.
Retrocopy TVLAPQPLGTKPLLPR--EMGTPVTSS-STASSN>QKVSASSKALFPSTAEAQAAVQGSVGTDFKPINSI

Parental  PATTTEPPKPTFPAYTQSTASTTSTTNSTAAKPA-ASITSKPATLTTTSATSKLIHPDEDISLEERRAQL
          PA.TTEP.KPTFPAYTQST.S.T.TTNSTA.K.A..S.TSKPATL.T.SA.SKLI.PDED.SLEERRAQL
Retrocopy PAITTEPAKPTFPAYTQSTVSITNTTNSTATKAA<TSVTSKPATLKTSSAISKLIYPDEDTSLEERRAQL

Parental  PKYQRNLPRPGQAPIGNPPVGPIGGMMPPQPGIPQQQGMRPPMPPHGQYGGHHQGMPGYLPSAMPPYGQ-
          .K.Q.NLP.PGQA.I.NP.V..I.G.M.P....P.QQGMRPPMPP.GQYG.HHQGMPGYLPSAMPP..Q.
Retrocopy SKHQSNLP*PGQASITNPAVVFI-GSMMP----P*QQGMRPPMPPLGQYGSHHQGMPGYLPSAMPPHVQ<

Parental  GPPMVPPYQGGPPRPPMGMRPPVMSQ
          GPPMVPP.....PR.P.GMR.PV..Q
Retrocopy GPPMVPPNCDRTPRRPVGMRSPVVLQ

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	57.52 RPM
SRP017611_kidney	0.00 RPM	71.29 RPM
SRP017611_liver	0.04 RPM	40.87 RPM
SRP040447_lung	0.00 RPM	94.53 RPM
SRP040447_skeletal_muscle	0.00 RPM	48.09 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1464 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1464 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001728	1 retrocopy	retro_cpor_1464 ,
Echinops telfairi	ENSETEG00000003828	1 retrocopy	retro_etel_883,
Homo sapiens	ENSG00000010244	1 retrocopy	retro_hsap_2373,
Myotis lucifugus	ENSMLUG00000016085	1 retrocopy	retro_mluc_322,
Nomascus leucogenys	ENSNLEG00000005954	1 retrocopy	retro_nleu_362,
Otolemur garnettii	ENSOGAG00000001200	2 retrocopies	retro_ogar_33, retro_ogar_751,
Pongo abelii	ENSPPYG00000008161	1 retrocopy	retro_pabe_2144,
Pan troglodytes	ENSPTRG00000008989	1 retrocopy	retro_ptro_1735,
Ictidomys tridecemlineatus	ENSSTOG00000000712	2 retrocopies	retro_itri_1800, retro_itri_1875,