RetrogeneDB ID: retro_pcap_386

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_645:132517..132930(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP1S2
• Ensembl ID: ENSPCAG00000000733
• Aliases: None
• Description: adaptor-related protein complex 1, sigma 2 subunit [Source:HGNC Symbol;Acc:560]

Sequence

>retro_pcap_386
CTGCTTTTCAGTGAGAGCGACCCTTCACCTGCAGAAACGGTATGTTCTATTATCTCTGGCAAAGATAAAAAAAAGATCAC
AAGGGAATTTGTTCAGGCCATTTTAGCACATAAACCTAAAAATGTACAGCTTTCTTGAGTGGCGAGATCTGAAGATTGTT
TACACAAGATAGGCCAGTTTGTATTCTTGATTGCGCTATCAAAGATCAAGACAATGAACTAATTACCCTGGAAATAATTT
ATCATTACTTGGAACTACTTGACAAGTATTTTGGCAGTGTAAGTGAACCTGACAGCATCTTTAATTTTGAGAAGGCATGT
TTTATTTCGGATGAGTTTCTTTAGGGAGGGGAAGGTCAGGAAACATCCACCGAAAATCTCCTCCAAGTAACTGAGCAGGC
AGATCTACTGCAG

Alignment

ORF - retro_pcap_386 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.19 %
• Parental protein coverage: 87.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLFSRQGKLRLQKWYVPLSDKEKKKITRELVQTVLARKPK-MCSFLEWRDLKIVYKRYASLY-FCCAIED
          LLFS..............S.K....ITRE.VQ..LA.KPK.M.SFLEWRDLKIVY.R.ASLY...CAI.D
Retrocopy LLFSESDPSPAETVCSIISGKDXXXITREFVQAILAHKPK>MYSFLEWRDLKIVYTR*ASLY>LDCAIKD

Parental  QDNELITLEIIHRYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEVQETSKKNVLKAIEQADLLQ
          QDNELITLEII..Y.ELLDKYFGSV.E.D.IFNFEKA.FI.DEFL.GGE.QETS..N.L...EQADLLQ
Retrocopy QDNELITLEIIYHYLELLDKYFGSVSEPDSIFNFEKACFISDEFL*GGEGQETSTENLLQVTEQADLLQ

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_386 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 16 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020420	1 retrocopy	retro_btau_1308,
Callithrix jacchus	ENSCJAG00000004393	1 retrocopy	retro_cjac_2312,
Dasypus novemcinctus	ENSDNOG00000013888	1 retrocopy	retro_dnov_1786,
Homo sapiens	ENSG00000182287	1 retrocopy	retro_hsap_1849,
Macaca mulatta	ENSMMUG00000014055	1 retrocopy	retro_mmul_1716,
Monodelphis domestica	ENSMODG00000017197	7 retrocopies	retro_mdom_1189, retro_mdom_1329, retro_mdom_1441, retro_mdom_1470, retro_mdom_1616, retro_mdom_1987, retro_mdom_903,
Otolemur garnettii	ENSOGAG00000011342	3 retrocopies	retro_ogar_2038, retro_ogar_265, retro_ogar_3453,
Procavia capensis	ENSPCAG00000000733	1 retrocopy	retro_pcap_386 ,
Pteropus vampyrus	ENSPVAG00000010218	1 retrocopy	retro_pvam_783,
Sorex araneus	ENSSARG00000000117	1 retrocopy	retro_sara_575,
Sarcophilus harrisii	ENSSHAG00000013119	2 retrocopies	retro_shar_651, retro_shar_690,
Sus scrofa	ENSSSCG00000012142	1 retrocopy	retro_sscr_998,
Ictidomys tridecemlineatus	ENSSTOG00000008517	1 retrocopy	retro_itri_131,
Tupaia belangeri	ENSTBEG00000008834	2 retrocopies	retro_tbel_2173, retro_tbel_4575,
Tarsius syrichta	ENSTSYG00000005290	2 retrocopies	retro_tsyr_1953, retro_tsyr_854,
Vicugna pacos	ENSVPAG00000007642	1 retrocopy	retro_vpac_596,