RetrogeneDB ID: retro_pcap_345

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_44707:15993..16866(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000007411
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BECN1
• Ensembl ID: ENSPCAG00000014049
• Aliases: None
• Description: beclin 1, autophagy related [Source:HGNC Symbol;Acc:1034]

Sequence

>retro_pcap_345
GAGACATCCGACATCTTCACCCTGCTGGGGAAGGTGTGCTCCATGCGAACGCTCAGCAGCATCCAGGAGACCTTCCTGGA
GGCATTCAACATCCTTTCTGGCGAGAAAGAAATGGATCACCCTTTGTGTGAGGAGTGCACTGACAGCCTCTTAGAGCTGC
TAGACATGCAACTCACCCGCACAGAATCTGAGTGTCAGATGTACAAACTCTGCTTGGAGACCAGGGAGCTGACAACATGT
CAGGAGGAGTTGGAGGTGCTGCAGAGAGAGCTGGAGAGCCTGGAGCTGGAGGAGGCGAGACTGGTCCAGGAGCTGGCTGG
TGTGGAGAAGGTCTGGAAACAGGCTGCAGGAGATCTCCAGGCCGCCCAGGCAGAGGCTGAGACACTAGAGCAGCAGGAGA
AACAGTCCTGGAGGGACTACAGCGTCTTGGAGCAGCAACAACTGGAGCTCTTGGATGAACTGAGGAGCTTGGAGAACCGG
CTGCAGGGCGCCCGGATCCAGCTGGGCCAACTGACCGACGCCAGCATCTTCCGCATGGCGTTTCACATCTGGCATGAGGG
CCCCGTCGGCGTCATCAACAACTTCAAGTTGGGCTGCCTTCCCACTGTCCCCGTGAGCTGGAGTGAGATCAGTGCTGCCT
GGGGGCAGACGGCTCTGCTGCTCTTTGTTCTGTCCAAGAAAATAGGACTGCAATTTCAGAGGTATAGACTTGTCCCCTTG
GGAAGCCATTCCTATCTGAAGCCTCTGACGGATGACTCGGCAGGGCTGCCATTGTTCTGTTTCCAGAAGCAGACTGTTTT
CTTGGATAAGTTTGACCATGCGATGGTGGCTTTCCTGGACTGTTTGCAGCAATTAAAGGAAAAGGTTGAGAAA

Alignment

ORF - retro_pcap_345 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.92 %
• Parental protein coverage: 75.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESANSFTLIGEASDGGTMENLSRRLKVTGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQN
          E....FTL.G.......M..LS.........F.I.SG....DHPLCEECTD.LL..LD.QL..TE.ECQ.
Retrocopy ETSDIFTLLGKVC---SMRTLSSIQETFLEAFNILSGEKEMDHPLCEECTDSLLELLDMQLTRTESECQM

Parental  YKRCLEILEQMN-EDDSEQLQMELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDHEEAQYQ
          YK.CLE..E........E.LQ.EL..L.LEE.RL.QEL..VEK..K..A..L...QAEAE.L...E.Q..
Retrocopy YKLCLETRELTTCQEELEVLQRELESLELEEARLVQELAGVEKVWKQAAGDLQAAQAEAETLEQQEKQSW

Parental  REYSEFKRQQLELDDELKSVENQMRYAQMQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEW
          R.YS....QQLEL.DEL.S.EN....A..QL..L.....F...FHIWH.G..G.INNF.LG.LP.VPV.W
Retrocopy RDYSVLEQQQLELLDELRSLENRLQGARIQLGQLTDASIFRMAFHIWHEGPVGVINNFKLGCLPTVPVSW

Parental  NEINAAWGQTVLLLHALANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMV
          .EI.AAWGQT.LLL..L..K.GL.FQRYRLVP.G.HSYL..LTD.S..LPL.C......F.D.KFDHAMV
Retrocopy SEISAAWGQTALLLFVLSKKIGLQFQRYRLVPLGSHSYLKPLTDDSAGLPLFCFQKQTVFLD-KFDHAMV

Parental  AFLDCVQQFKEEVEK
          AFLDC.QQ.KE.VEK
Retrocopy AFLDCLQQLKEKVEK

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_345 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 17 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006867	1 retrocopy	retro_amel_16,
Bos taurus	ENSBTAG00000019914	1 retrocopy	retro_btau_226,
Dipodomys ordii	ENSDORG00000000956	1 retrocopy	retro_dord_675,
Felis catus	ENSFCAG00000013136	1 retrocopy	retro_fcat_62,
Homo sapiens	ENSG00000126581	1 retrocopy	retro_hsap_335,
Macropus eugenii	ENSMEUG00000011700	1 retrocopy	retro_meug_600,
Macaca mulatta	ENSMMUG00000029971	1 retrocopy	retro_mmul_81,
Monodelphis domestica	ENSMODG00000015064	1 retrocopy	retro_mdom_1778,
Mus musculus	ENSMUSG00000035086	1 retrocopy	retro_mmus_390,
Nomascus leucogenys	ENSNLEG00000011840	1 retrocopy	retro_nleu_1776,
Oryctolagus cuniculus	ENSOCUG00000015964	3 retrocopies	retro_ocun_1021, retro_ocun_1732, retro_ocun_218,
Procavia capensis	ENSPCAG00000014049	1 retrocopy	retro_pcap_345 ,
Pan troglodytes	ENSPTRG00000022819	1 retrocopy	retro_ptro_268,
Sorex araneus	ENSSARG00000000367	1 retrocopy	retro_sara_136,
Sus scrofa	ENSSSCG00000017386	1 retrocopy	retro_sscr_75,
Ictidomys tridecemlineatus	ENSSTOG00000012612	1 retrocopy	retro_itri_25,
Tursiops truncatus	ENSTTRG00000011716	1 retrocopy	retro_ttru_595,