RetrogeneDB ID: retro_cpor_704

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_24:13492903..13493270(-)
• Located in intron of: ENSCPOG00000004478

Retrocopy information

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

Parental gene information

• Parental gene symbol: LITAF
• Ensembl ID: ENSCPOG00000006659
• Aliases: None
• Description: None

Sequence

>retro_cpor_704
CCTGTGCCTGGCCAGCCACAGGGCCCACGATAGGCGAAGTCTGGAAGAGCACACATCCTCCTTCCGCAGATATATAGCTG
GTGCCCTGCCCCAGTGTCAATGCGACTGCTGCACAGACCATCTCCATGCAGCAGTTAATTTTCCTTTTGACCACCCCAGG
CCAGGTGTGCTGTCCTTCCTGCAACAAGATGATCATGACACAGCTGTCCTACGATGCTGGTGTTCTCACTTGACTCTTCT
GTGGGAGCCTGTGCCTACTGGAGTGCACAACAGGGTGCAGCTTCATCCCTTTCAGTGAGGGTACCCTGCAGGGCATGGAC
CACTACTGTGCTAAAGGCAAAACCTCTTGGGCACTTCTAAGATCTTG

Alignment

ORF - retro_cpor_704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.54 %
• Parental protein coverage: 76.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PVPG-PTTGLMTGPDGKGANPPLYYTQPVPVLNPSANTTV-QTVFVQQPVSFFDRPVQMCCPSCNKMVVT
          PVPG.P.TG...G...K...PP......VP...PS.N.T..QT...QQ.......P.Q.CCPSCNKM..T
Retrocopy PVPG<PATGPTIGEVWKSTHPPSADI*LVPC--PSVNATAAQTISMQQLIFLLTTPGQVCCPSCNKMIMT

Parental  KLSYNAGVLTWLSCGSLCLLGCVLGCCFIPFCVDALQDVDHYCPNCKA-LLGTYKRL
          .LSY.AGVLT.L.CGSLCLL.C..GC.FIPF....LQ..DHYC...K..LLGT.K.L
Retrocopy QLSYDAGVLT*LFCGSLCLLECTTGCSFIPFSEGTLQGMDHYCAKGKT<LLGTSKIL

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	0.17 RPM	8.97 RPM
SRP017611_kidney	0.00 RPM	8.06 RPM
SRP017611_liver	0.04 RPM	12.10 RPM
SRP040447_lung	0.00 RPM	59.92 RPM
SRP040447_skeletal_muscle	0.03 RPM	9.48 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_704 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_704 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006659	1 retrocopy	retro_cpor_704 ,
Macaca mulatta	ENSMMUG00000008784	1 retrocopy	retro_mmul_1411,
Monodelphis domestica	ENSMODG00000005014	4 retrocopies	retro_mdom_174, retro_mdom_574, retro_mdom_887, retro_mdom_911,
Otolemur garnettii	ENSOGAG00000028239	2 retrocopies	retro_ogar_1479, retro_ogar_2820,
Pteropus vampyrus	ENSPVAG00000009213	1 retrocopy	retro_pvam_261,
Rattus norvegicus	ENSRNOG00000002520	1 retrocopy	retro_rnor_2056,
Tupaia belangeri	ENSTBEG00000017097	1 retrocopy	retro_tbel_4388,
Tursiops truncatus	ENSTTRG00000010854	1 retrocopy	retro_ttru_1244,