RetrogeneDB ID: retro_tbel_3543

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_144276:248622..249134(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDAP1
• Ensembl ID: ENSTBEG00000010152
• Aliases: None
• Description: PDGFA associated protein 1 [Source:HGNC Symbol;Acc:14634]

Sequence

>retro_tbel_3543
CCCAACGGAGGGAGGAAGGGAGGTGGCAAGGCCGGGCAAGGCCGCCCGCGAGCCCTGAGGAGATGGACGCACAGCTCCAG
GCCGAAAAGCAGAAAGCCAGGGAAGAAGAGGAACAAGAAGTTGAGCTGAGGCTGCAGGTGTCCCCAGAAAGGGAAGAAAT
CTCTAGACTCAGATGAGAGTGAGGATGAAGAAGATGACTACCAGCAAAAGCTCAAAGGCTGGAAGGGCTATTGACATGGA
GACCCCCCACCCGGTGGCCCAGACAGCCAAAACGGTCACACACCTAGGTCTGGACGAGCCAAAGGAGCTTTCAAGAAGAG
AATGAGAAGAAATTGAGAAACAGAAAGCAAGAGAGCATGCCATGAAAATGCATTTAGCTGGGAAAACAGAGCAAGTCAAG
GCCAACCTTGCCTGGCGACTGTCATCTGGAAACAGTGGGAGGAGGCCACAAGGAGGAAATGAGAGGAGAGGAAAGCAATA
GATGATGCACTTTGTCAGGAAAGCAGATGCAG

Alignment

ORF - retro_tbel_3543 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.34 %
• Parental protein coverage: 99.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PKGGRKGGHKGRARQYTSPEEIDAQLQAEKQKAREEEEEEEEGGDGAAGDPKKEKKSLDSDESEDEEDDY
          P.GGRKGG..G.A.Q...P............K.R................P.K.KKSLDSDESEDEEDDY
Retrocopy PNGGRKGG--GKAGQ-GRPRALRRWTHSSRPKSRKPGKKRNKKLS*GCRCPQKGKKSLDSDESEDEEDDY

Parental  QQKRKG-VEGL-IDIENPNRVAQTTKKVTQLDLDGPKELSRREREEIEKQKAKERYMKMHLAGKTEQAKA
          QQK.KG..EGL.ID.E.P..VAQT.K.VT.L.LD.PKELSRRE.EEIEKQKA.E..MKMHLAGKTEQ.KA
Retrocopy QQKLKG<LEGL<IDMETPHPVAQTAKTVTHLGLDEPKELSRRE*EEIEKQKAREHAMKMHLAGKTEQVKA

Parental  DLA-RLAIIRKQREEAARKKEEERKAKDDA-TLSGKRMQ
          .LA.....I.KQ.EEA.R.K.EERKA.DDA.TLSGK.MQ
Retrocopy NLA<LATVIWKQWEEATRRK*EERKAIDDA<TLSGKQMQ

Legend:

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

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_3543 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3543 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015838	2 retrocopies	retro_cjac_2676, retro_cjac_2725,
Equus caballus	ENSECAG00000024426	1 retrocopy	retro_ecab_449,
Echinops telfairi	ENSETEG00000009926	1 retrocopy	retro_etel_900,
Felis catus	ENSFCAG00000015067	1 retrocopy	retro_fcat_1227,
Homo sapiens	ENSG00000106244	3 retrocopies	retro_hsap_1061, retro_hsap_3210, retro_hsap_3506,
Gorilla gorilla	ENSGGOG00000025196	5 retrocopies	retro_ggor_1776, retro_ggor_1778, retro_ggor_2179, retro_ggor_2371, retro_ggor_837,
Macaca mulatta	ENSMMUG00000001460	2 retrocopies	retro_mmul_1865, retro_mmul_943,
Mus musculus	ENSMUSG00000029623	1 retrocopy	retro_mmus_2581,
Nomascus leucogenys	ENSNLEG00000011017	1 retrocopy	retro_nleu_1158,
Otolemur garnettii	ENSOGAG00000010874	2 retrocopies	retro_ogar_2199, retro_ogar_789,
Ochotona princeps	ENSOPRG00000013615	2 retrocopies	retro_opri_262, retro_opri_512,
Pongo abelii	ENSPPYG00000017375	4 retrocopies	retro_pabe_2659, retro_pabe_2806, retro_pabe_2901, retro_pabe_884,
Pan troglodytes	ENSPTRG00000041711	4 retrocopies	retro_ptro_1711, retro_ptro_2240, retro_ptro_2378, retro_ptro_722,
Ictidomys tridecemlineatus	ENSSTOG00000001679	1 retrocopy	retro_itri_765,
Tupaia belangeri	ENSTBEG00000010152	5 retrocopies	retro_tbel_1365, retro_tbel_3543 , retro_tbel_4066, retro_tbel_766, retro_tbel_975,
Tursiops truncatus	ENSTTRG00000003004	1 retrocopy	retro_ttru_1343,