RetrogeneDB ID: retro_tbel_1331

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4409:106421..107535(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SERBP1
• Ensembl ID: ENSTBEG00000003689
• Aliases: None
• Description: SERPINE1 mRNA binding protein 1 [Source:HGNC Symbol;Acc:17860]

Sequence

>retro_tbel_1331
GTCACCAACCAACTGGACCAGTTATTGGACGATGAATTGGACCCCTTTGAGGTGCTGAAAGCAGCAGAGAACAAGAAAAA
AGAAGCTTGCGGGGGGTAGCATTGGGGACCCTGGGGCCAAGAGCGCAGCTCAGGCTGCAGTCCAGACCAACTCTAAAGCA
GTAAACAGCTGAAAAAAGGAGTCACAGAAAGACCACAAGAACCTGCTGCCCTCCTGACAACAGCGTGACTGATAAGGAGA
AGAGACAGCTGCCTATGGCACTTAAGAAAGAAGGAATAAGACGTGTTAGAAGGTGACCTAATCAACAACTAGGGGGTGAT
GGGGAAATAATTGATAGGAGACCAGAAAGGCGACTGCCACGTGAAAGGAGATTTGAAAAGCCACTTGAAGAAATGGGTGA
AGGAAGTGAATTTTCAGTTGATAGACCTGTAATTGACCAACCTATTCGAGGCCGTGGTGGTCTTGGAAGAGGTCAAGGAG
GCCATGGACGTGAAATGGGCCAAGGAGATGGATTTGATTCCCATGGCAAGCATGAATTTGATAGGCATAGTGGGAATGAG
AGATCTTCTTTTTCACATTACAGTGGCCTGAAGCATGAGGACAAACATGGAGGTAATGGATCTCACAACTGGGGAACTGT
CAAAGATGAATTAACAGAGTACCCCAAATACATTTAGAAACCAATATCTTATCATTGCAGTGACTTGGATCAATCATCTG
TGACTGAGGAAACACCTGAGGACAAAGAACATCCAGTGGCAGACACTGAAAATAAGGAAAATGAGGTTGAAGAGGTAAAG
GAAGAAAGTCCAAAGGAGATGACTTTGGATGAATGGAAGGCTATTCAAAATAAGGACCAGGCAGAAGTAGAATTTAATAT
TCAAAAACCAAACGAAGGTGCTGATGGACAGTGGAAGAAGGGATTTGTTCTTCATAAATCAAAGAGTAAGAGGCTCATGC
TGAAGTTTCAGTTATGGACCATCATTTCCGGAAGCGAGCAAATGATATGATATCTCACCTGGAGATCAATTTTGGAGACC
TTGGCTGCCCAGGACGTGGTGGCAGGGGAGGATGAGGTGGGCGTGGTGGACATCCAAACTGTGGCAGCAGCACC

Alignment

ORF - retro_tbel_1331 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.64 %
• Parental protein coverage: 92.33 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VTNRFDQLFDDESDPFEVLKAAENKKKEA-GGGGVGGPGAKSAAQAA-QTSNAAGKPLRKESQKDRKNPL
          VTN..DQL.DDE.DPFEVLKAAENKKKEA..GG..G.PGAKSAAQAA.QT...A.....KESQKD.KN.L
Retrocopy VTNQLDQLLDDELDPFEVLKAAENKKKEA>AGGSIGDPGAKSAAQAAVQTNSKAVNS*KKESQKDHKNLL

Parental  P-PNVGVTDKKEETHPPVALKKEGIRRVGRRPDQQLQGDGKIIDRRPERRLPRERRFEKPLEEKGEGGEF
          P.P...VTDK.E....P.ALKKEGIRRV.R.P.QQL.GDG.IIDRRPERRLPRERRFEKPLEE.GEG.EF
Retrocopy P>PDNSVTDK-EKRQLPMALKKEGIRRVRR*PNQQLGGDGEIIDRRPERRLPRERRFEKPLEEMGEGSEF

Parental  SVDRPIIDRPIRGRGGLGRGRGGRGRGMGRGDGFDSRGKREFDRHSGSDRSSFSHYSGLKHEDKRGGSGS
          SVDRP.ID.PIRGRGGLGRG.GG.GR.MG.GDGFDS.GK.EFDRHSG..RSSFSHYSGLKHEDK.GG.GS
Retrocopy SVDRPVIDQPIRGRGGLGRGQGGHGREMGQGDGFDSHGKHEFDRHSGNERSSFSHYSGLKHEDKHGGNGS

Parental  HNWGTVKDELTESPKYIQKPISYNCSDLDQSTVTEETPEGEEHPVADTENKENEVEEVKEEGPKEMTLDE
          HNWGTVKDELTE.PKYI.KPISY.CSDLDQS.VTEETPE..EHPVADTENKENEVEEVKEE.PKEMTLDE
Retrocopy HNWGTVKDELTEYPKYI*KPISYHCSDLDQSSVTEETPEDKEHPVADTENKENEVEEVKEESPKEMTLDE

Parental  WKAIQNKDRAKVEFNIRKPNEGADGQWKKGFVLHKSKSE-EAHAEDSVMDHHFRKPANDITSQLEINFGD
          WKAIQNKD.A.VEFNI.KPNEGADGQWKKGFVLHKSKS..EAHAE.SVMDHHFRK.AND..S.LEINFGD
Retrocopy WKAIQNKDQAEVEFNIQKPNEGADGQWKKGFVLHKSKSK<EAHAEVSVMDHHFRKRANDMISHLEINFGD

Parental  LGRPGRGGRGGRGGRGRGGRPNRGSRT
          LG.PGRGGRGG.G..GRGG.PN.GS.T
Retrocopy LGCPGRGGRGG*G--GRGGHPNCGSST

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_1331 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1331 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 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018538	1 retrocopy	retro_cfam_546,
Callithrix jacchus	ENSCJAG00000017440	2 retrocopies	retro_cjac_1207, retro_cjac_3015,
Homo sapiens	ENSG00000142864	3 retrocopies	retro_hsap_3056, retro_hsap_413, retro_hsap_4695,
Gorilla gorilla	ENSGGOG00000010396	1 retrocopy	retro_ggor_408,
Myotis lucifugus	ENSMLUG00000001424	1 retrocopy	retro_mluc_691,
Oryctolagus cuniculus	ENSOCUG00000008946	1 retrocopy	retro_ocun_1041,
Otolemur garnettii	ENSOGAG00000025884	1 retrocopy	retro_ogar_185,
Pongo abelii	ENSPPYG00000001256	1 retrocopy	retro_pabe_3790,
Pan troglodytes	ENSPTRG00000023560	2 retrocopies	retro_ptro_1985, retro_ptro_317,
Sorex araneus	ENSSARG00000000803	1 retrocopy	retro_sara_135,
Tupaia belangeri	ENSTBEG00000003689	4 retrocopies	retro_tbel_1004, retro_tbel_1331 , retro_tbel_2427, retro_tbel_532,