RetrogeneDB ID: retro_pcap_430

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_85108:329..1010(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCTN2
• Ensembl ID: ENSPCAG00000016236
• Aliases: None
• Description: dynactin 2 (p50) [Source:HGNC Symbol;Acc:2712]

Sequence

>retro_pcap_430
TTCTCACATTGTATTGGAAAAATCAAGGAGTCAAGATATGAATCTGGAGACAATGAGAAGAGTGGTAAGGGCCTGGGAGT
AAAGCAGACACCTTAGCAGAAGTGCCAGCAACTACTTCATGAGGGCCAAGAGCTGACAACTGAAGCTGAGAAATTCAAGA
CTACAGCGAAGGAGTCAGCCACAGAGGGGAACCTGATGTCTGTGGTGCAGGCTAAACAGCAGGCAGCACTGAAGCAGCAA
ATCGCTGCTTCCCAACTGAAGAAACTGCTGGGACCAGATGCTGCAGTCAAACTCATTGACCCAATGGGGCTCTGGCTAAG
CACCTGCTACTGAAGCCAGAAGCAACCAAGGACAGCAAAGGCGTCGTCCAGGGGGAAAGACTACCAGTAGGATCCTTCCA
CAAAGCAGCCCTGTCACTTATGAACTACATTCCGGGCCTGAAAAAGGATGAGCGACCTGAAGCTGTCAATGCTGCAGAAC
CTGGTAAGCACCCTACAGAGCTGGAGACAACTGTACACTGCGATCAGGATGCTCAGAGTCTCCTTTCTGCAGCCCCCAGG
GAGCCTGTCTTTAAAAGACTGAAGAGGGAAAGGTGACTTCCTGGACCTTGCAGCTTTGGACCAAATGAAGGCGTGGCTAC
AGAGTGTAGCCATGCCAACAGTGAATAAGATCGCCAAGCAT

Alignment

ORF - retro_pcap_430 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.29 %
• Parental protein coverage: 56.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  FSDRIGKTKRTGYESGDYEMLGEGLGIKETPQQKYQRLLHEVQELTTEVEKIKTTVKESATEEKLTPVVL
          FS..IGK.K...YESGD.E..G.GLG.K.TP.QK.Q.LLHE.QELTTE.EK.KTT.KESATE..L..VV.
Retrocopy FSHCIGKIKESRYESGDNEKSGKGLGVKQTP*QKCQQLLHEGQELTTEAEKFKTTAKESATEGNLMSVVQ

Parental  AKQLAALKQQLVASHLEKLLGPDAAINLTD-PDGALAKRLLLQLEATKNSKGT-GSGGKTSSGALPDSSL
          AKQ.AALKQQ..AS.L.KLLGPDAA..L.D.P.GALAK.LLL..EATK.SKG....GGKT.S..LP.SS.
Retrocopy AKQQAALKQQIAASQLKKLLGPDAAVKLID<PNGALAKHLLLKPEATKDSKGV<RPGGKTTSRILPQSSP

Parental  VTYELHSRPE-QDKFSQAAKVAELEKRLTELEATVRCDQDAQNPLSA-GLQGACLMETVELLQAKVSALD
          VTYELHS.PE..D....A...AE..K..TELE.TV.CDQDAQ..LSA...QGACL..T.E....KV....
Retrocopy VTYELHSGPE>KDERPEAVNAAEPGKHPTELETTVHCDQDAQSLLSA<SPQGACL*KTEE---GKVTSWT

Parental  L-AVLDQVEARLQSV-LGKVNEIAKH
          L.A.LDQ..A.LQSV....VN.IAKH
Retrocopy L<AALDQMKAWLQSVAMPTVNKIAKH

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_430 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000233	3 retrocopies	retro_cfam_1095, retro_cfam_385, retro_cfam_579,
Dipodomys ordii	ENSDORG00000007137	1 retrocopy	retro_dord_441,
Loxodonta africana	ENSLAFG00000013538	1 retrocopy	retro_lafr_312,
Mustela putorius furo	ENSMPUG00000001840	1 retrocopy	retro_mputfur_197,
Procavia capensis	ENSPCAG00000016236	1 retrocopy	retro_pcap_430 ,