RetrogeneDB ID: retro_tbel_979

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3492:25774..26258(-)
• Located in intron of: ENSTBEG00000013780

Retrocopy information

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

Parental gene information

• Parental gene symbol: PBDC1
• Ensembl ID: ENSTBEG00000003411
• Aliases: None
• Description: polysaccharide biosynthesis domain containing 1 [Source:HGNC Symbol;Acc:28790]

Sequence

>retro_tbel_979
ATGGAGGCTACGAGAGGTCCTGAGGAGCCGGCTGCCGGGGAGCTGGTGGCTATGGCACGTGCTCTTTCTCTCGCAGCAGA
ATCAGGTGGCAGCGACCCTGACGCTGAGACGGCCAGGCCGTGAGGGCGATGCAGCATGCTGAAATCTATTACAAGCTGAT
GTCATCGGCTCACCCACGGTTCCTGAAACTCACCAAAGTGGATGACCAAATCCACTCTGAGTTCGGGGAATTTTCGAGAA
ACTCAAGACAGATGTACCAGATCCAGAACAACTCAAATCAGAGTCAGCTAAAGAGAAGTGGAGCCCGTTCTGCATGAACT
TTGATGGGACTACAGAAGACTTCAGCTGTGGGACTTTGTTACAACTAGATTGTTCTCAGGGCTACACTGAGGAAAACATC
TTTCCCCCCAGGGTTCAATTTTCTGCCACTGAAATTGCTGAAAACCAGGAAGGCTATAACAAAGCAGTTTATATCAGTGT
TCAG

Alignment

ORF - retro_tbel_979 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.51 %
• Parental protein coverage: 72.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEASSGTDE-VSGELLSVAHALSLPAESYGNDPDIEMA-WAMRAMQHAEVYYKLISSVDPQFLKLTKVDD
          MEA..G..E...GEL...A.ALSL.AES.G.DPD.E.A..A.RAMQHAE.YYKL.SS..P.FLKLTKVDD
Retrocopy MEATRGPEEPAAGELVAMARALSLAAESGGSDPDAETA<QAVRAMQHAEIYYKLMSSAHPRFLKLTKVDD

Parental  QIYSEFRE-IFEKLRIDVLDPEELKSESAKEKWRPFCMKFDGIVEDFNYGTLLRLDSQ--YTEETI-APR
          QI.SEF.E.IFEKL..DV.DPE.LKSESAKEKW.PFCM.FDG..EDF..GTLL.LD....YTEE.I..PR
Retrocopy QIHSEFGE<IFEKLKTDVPDPEQLKSESAKEKWSPFCMNFDGTTEDFSCGTLLQLDCSQGYTEENIFPPR

Parental  IQFFAIEIARNREGYNKAVYISVQ
          .QF.A.EIA.N.EGYNKAVYISVQ
Retrocopy VQFSATEIAENQEGYNKAVYISVQ

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_979 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_979 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017228	2 retrocopies	retro_cfam_1588, retro_cfam_944,
Callithrix jacchus	ENSCJAG00000018571	1 retrocopy	retro_cjac_1880,
Equus caballus	ENSECAG00000009882	1 retrocopy	retro_ecab_532,
Erinaceus europaeus	ENSEEUG00000001116	1 retrocopy	retro_eeur_377,
Monodelphis domestica	ENSMODG00000009685	2 retrocopies	retro_mdom_1002, retro_mdom_572,
Mus musculus	ENSMUSG00000031226	1 retrocopy	retro_mmus_1569,
Oryctolagus cuniculus	ENSOCUG00000001088	3 retrocopies	retro_ocun_1017, retro_ocun_1402, retro_ocun_595,
Otolemur garnettii	ENSOGAG00000015205	1 retrocopy	retro_ogar_3063,
Rattus norvegicus	ENSRNOG00000002662	3 retrocopies	retro_rnor_1703, retro_rnor_1705, retro_rnor_826,
Sarcophilus harrisii	ENSSHAG00000017872	1 retrocopy	retro_shar_132,
Tupaia belangeri	ENSTBEG00000003411	3 retrocopies	retro_tbel_3448, retro_tbel_494, retro_tbel_979 ,