RetrogeneDB ID: retro_cpor_1170

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_52:11548540..11549062(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUCLG1
• Ensembl ID: ENSCPOG00000003017
• Aliases: None
• Description: None

Sequence

>retro_cpor_1170
AATCGGCCCAGAGTCATCAGTCCTGGAGAATGCAAAATTGGCATCATGCCTGGCCATATTCACAAGAACGAAAGAGTCAG
TGTTGTGTCCACATAGGGCACCTGACTTATGAAGCAGTTCATCAGACAACAAAAGTTGGATTGGGACAGTCTTTGTGTGT
TGGCATTGAAGGTAATCCTTTAATGGAACACATTTTATTGACTTCCTTGAAATCTTTCTGAGTGACCCAGCCACAGAAGA
CATCACATTGATTGGTGAAATTGGTGACAGTGCAGAAGAAAATGCTGCAGAATTTTTGAAGCAACATAATTCTGGTCCAA
ATGCCAAGCCTGTAGTGCCCTTCATTGCTGGTCTAACTGCACCTCCTAGGAGAAGAATGGGTCACTCGGGCCATTATTAC
TGGAGGGAAAGGTGGAGCTCAAAAGAAGATTGCTGCCCTTGAGTGCAGGCATCATGGTCAGCATATTGCCTGCACAGCTG
GGGACCATCATCTACAAGGAATTTGAAAAGAGAACAATACTA

Alignment

ORF - retro_cpor_1170 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.59 %
• Parental protein coverage: 50.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  NCPGVINPGECKIGIMPGHIHKKGRVGIVSRSGT-LTYEAVHQTTQVGLGQSLCVGIGGDP-FNGTDFID
          N.P.VI.PGECKIGIMPGHIHK..RV..VS..GT.LTYEAVHQTT.VGLGQSLCVGI.G.P.FNGT.FID
Retrocopy NRPRVISPGECKIGIMPGHIHKNERVSVVST*GT<LTYEAVHQTTKVGLGQSLCVGIEGNP<FNGTHFID

Parental  CLDIFLRDSGTEGIILIGEIGGNAEENAAEFLKQHNSGPNAKPVVSFIAGLTAPPGRRM-GHAG-AIIAG
          .L.IFL.D..TE.I.LIGEIG..AEENAAEFLKQHNSGPNAKPVV.FIAGLTAPP.RRM.G..G.AII.G
Retrocopy FLEIFLSDPATEDITLIGEIGDSAEENAAEFLKQHNSGPNAKPVVPFIAGLTAPPRRRM<GSLG<AIITG

Parental  GKGGA-KEKIAALQSAGVVISMSPAQLGTTIYKEFEKRKML
          GKGGA.K.....L.SAG...S..PAQLGT.IYKEFEKR..L
Retrocopy GKGGA>KRRLLPL-SAGIMVSILPAQLGTIIYKEFEKRTIL

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	0.29 RPM	61.37 RPM
SRP017611_kidney	0.10 RPM	365.88 RPM
SRP017611_liver	0.00 RPM	120.83 RPM
SRP040447_lung	0.13 RPM	71.50 RPM
SRP040447_skeletal_muscle	0.03 RPM	292.49 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1170 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1170 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003017	1 retrocopy	retro_cpor_1170 ,
Myotis lucifugus	ENSMLUG00000012370	1 retrocopy	retro_mluc_1231,
Procavia capensis	ENSPCAG00000013405	1 retrocopy	retro_pcap_356,
Pteropus vampyrus	ENSPVAG00000003656	2 retrocopies	retro_pvam_1160, retro_pvam_670,
Drosophila melanogaster	FBgn0004888	1 retrocopy	retro_dmel_47,