RetrogeneDB ID: retro_cpor_763

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_27:6481429..6481854(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIPRL
• Ensembl ID: ENSCPOG00000009945
• Aliases: None
• Description: None

Sequence

>retro_cpor_763
GCCCACATCGTGAAGTTAGTGGATGAATTGCAATATGCCATCTCTCCCGAAATGATGTTTGGAGACAACGTTTTAAGAAT
CCAACATGGTTCTGGCTTTGAGGATTGAGTTCAGTGCTACAGATGCATTAAAAATGTGTAAACAATTACCAAGGAATGCT
TAAAGTAGCTTGTGCTGAAGAGTGGCAGGAAAGAAGGATGTAAGGGGAGCATTCTAAAGACGTTGTTAAACCATGCGATT
GGACCTATATAACAGATTATAAAGGAGCACTACTTGGTGACTCTCTTAAATTAAAGGTTCTACCTACAACAGATCATATA
GATACAGAGAAATTGAAAGCCAGAGAACAGATTACATTTTTTGAAGAAGTTCTTCTCTTTGAGGATGAACTTCATGATCA
TGGAGTTTCAAGCCTGCATGTGAAA

Alignment

ORF - retro_cpor_763 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.92 %
• Parental protein coverage: 51.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ADVEKLADELHMPSLPEMMFGDNVLRIQHGSGFG-IEFNATDAL-KCVNNYQGMLKVACAEEWQESRTEG
          A...KL.DEL.....PEMMFGDNVLRIQHGSGF..IEF.ATDAL.KCVNNYQGMLKVACAEEWQE.R..G
Retrocopy AHIVKLVDELQYAISPEMMFGDNVLRIQHGSGFE>IEFSATDAL>KCVNNYQGMLKVACAEEWQERRM*G

Parental  EHSKEVVKPYDWTYTTDYKGTLLGDSLKLKVVPTTDHIDTEKLKAREQIKFFEEVLLFEDELHDHGVSSL
          EHSK.VVKP.DWTY.TDYKG.LLGDSLKLKV.PTTDHIDTEKLKAREQI.FFEEVLLFEDELHDHGVSSL
Retrocopy EHSKDVVKPCDWTYITDYKGALLGDSLKLKVLPTTDHIDTEKLKAREQITFFEEVLLFEDELHDHGVSSL

Parental  SVK
          .VK
Retrocopy HVK

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	25.25 RPM
SRP017611_kidney	0.00 RPM	18.95 RPM
SRP017611_liver	0.00 RPM	14.28 RPM
SRP040447_lung	0.00 RPM	10.64 RPM
SRP040447_skeletal_muscle	0.05 RPM	9.96 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_763 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_763 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 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008689	3 retrocopies	retro_chof_1079, retro_chof_1094, retro_chof_1746,
Cavia porcellus	ENSCPOG00000009945	1 retrocopy	retro_cpor_763 ,
Echinops telfairi	ENSETEG00000005808	1 retrocopy	retro_etel_1273,
Microcebus murinus	ENSMICG00000007808	1 retrocopy	retro_mmur_1335,
Myotis lucifugus	ENSMLUG00000011927	3 retrocopies	retro_mluc_607, retro_mluc_909, retro_mluc_941,
Monodelphis domestica	ENSMODG00000002880	1 retrocopy	retro_mdom_180,
Mus musculus	ENSMUSG00000040843	1 retrocopy	retro_mmus_2653,
Ochotona princeps	ENSOPRG00000011313	1 retrocopy	retro_opri_885,
Pteropus vampyrus	ENSPVAG00000005071	1 retrocopy	retro_pvam_257,
Rattus norvegicus	ENSRNOG00000003048	1 retrocopy	retro_rnor_2197,
Sarcophilus harrisii	ENSSHAG00000018932	1 retrocopy	retro_shar_771,
Ictidomys tridecemlineatus	ENSSTOG00000014921	1 retrocopy	retro_itri_1756,
Tupaia belangeri	ENSTBEG00000017081	3 retrocopies	retro_tbel_1717, retro_tbel_2833, retro_tbel_3376,