RetrogeneDB ID: retro_pcap_139

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_103321:3..346(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSR4
• Ensembl ID: ENSPCAG00000009037
• Aliases: None
• Description: signal sequence receptor, delta [Source:HGNC Symbol;Acc:11326]

Sequence

>retro_pcap_139
ATGGCGGTGGTAGCACCTCCTGGGGCCCTGGCACTCCTCCTGCTGTCTGGCCTCTCCTGCTGCTCAGCAGAGGCCTGCTT
GGAGCCCCAGATCACACCCTCCTATTACACCACCTCGGACGCCGTCATCGCCAGTGAGACGGTCTTCATCATGGAGATCT
CCCTGACCTGCAAGAACCAGGTCCAGAACATGGCTCTTTATGCTGACATCAGTGGAAAACAATTTCCTGTCACCTGGGGC
CAGGATGTTGGGCGTTACCAGGTGTCCTGGAGCCTAGACCACAAAAGCACTACATGCGGGTACCTAAGAGGTCAGATTCT
TCGATGAGGAGTCATACAGTCTC

Alignment

ORF - retro_pcap_139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.3 %
• Parental protein coverage: 65.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAVAPLGALALLLLSGLSCCSAEACLEPQITPSYYTTSDAVIATETVFIVEISLTCKNRVQNMALYADV
          MA.VAP.GALALLLLSGLSCCSAEACLEPQITPSYYTTSDAVIA.ETVFI.EISLTCKN.VQNMALYAD.
Retrocopy MAVVAPPGALALLLLSGLSCCSAEACLEPQITPSYYTTSDAVIASETVFIMEISLTCKNQVQNMALYADI

Parental  SGKQFPVTRGQDVGRYQVSWSLDHKSA-HAGTYEVRFFDEESYSL
          SGKQFPVT.GQDVGRYQVSWSLDHKS..HAGT.EVRFFDEESYSL
Retrocopy SGKQFPVTWGQDVGRYQVSWSLDHKST>HAGT*EVRFFDEESYSL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_139 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011328	1 retrocopy	retro_acar_97,
Callithrix jacchus	ENSCJAG00000011167	1 retrocopy	retro_cjac_2056,
Dasypus novemcinctus	ENSDNOG00000025714	2 retrocopies	retro_dnov_1204, retro_dnov_922,
Homo sapiens	ENSG00000180879	1 retrocopy	retro_hsap_2536,
Gorilla gorilla	ENSGGOG00000024329	1 retrocopy	retro_ggor_1585,
Loxodonta africana	ENSLAFG00000006908	1 retrocopy	retro_lafr_337,
Mustela putorius furo	ENSMPUG00000008803	1 retrocopy	retro_mputfur_148,
Nomascus leucogenys	ENSNLEG00000013602	1 retrocopy	retro_nleu_2738,
Otolemur garnettii	ENSOGAG00000006738	1 retrocopy	retro_ogar_691,
Procavia capensis	ENSPCAG00000009037	1 retrocopy	retro_pcap_139 ,
Sus scrofa	ENSSSCG00000012784	1 retrocopy	retro_sscr_866,