RetrogeneDB ID: retro_tbel_1260

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4258:201897..202332(+)
• Located in intron of: ENSTBEG00000001981

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCCIP
• Ensembl ID: ENSTBEG00000002570
• Aliases: None
• Description: BRCA2 and CDKN1A interacting protein [Source:HGNC Symbol;Acc:978]

Sequence

>retro_tbel_1260
AGCAATGATGATATGGGTGAAGATGAGATTTTCAGTTTCGTAAGCTTTTTAAATTTAACTGAAAGAAAGGGTACCCAGTG
TGCTGAACAAGTTGAAGAGCTGATTCTAAGCCATTGTGAGAAGAACTGTGAAAAGAGCGTGGTTGAACAGCTGGACAAGG
TTTTAAATGACACTACCAAGCCTATAGGCTTTCTCCTCAGTGAAAGGTTCAGCAGTGTCCCTCCACAGGTCGCTCTGTCC
ATGTATCAGCAACTTCAGAAAGAACTAACAGAAGCACACAAAACTAGTAAGCCATGCGAGAAGTGCTACTTTTACCTTCT
GATTAGCAGGACATTTGTGGAAGCAGGAAAAAACAATTCCGAAAAGAAATGTTATATCCAAAAGAAAAATGAGTTAATGT
TCGCAAATGCAGAGGAAGAATTTTTCTACGGGAAG

Alignment

ORF - retro_tbel_1260 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.76 %
• Parental protein coverage: 83.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDDDMDEDEIFGFISLLNLTEKKGTQCAEQIKELILSCCEKNCEKSMVEQLDKVLNDTTKPVGFLLSERF
          S.DDM.EDEIF.F.S.LNLTE.KGTQCAEQ..ELILS.CEKNCEKS.VEQLDKVLNDTTKP.GFLLSERF
Retrocopy SNDDMGEDEIFSFVSFLNLTERKGTQCAEQVEELILSHCEKNCEKSVVEQLDKVLNDTTKPIGFLLSERF

Parental  INVPPQIALPMHQQLQKELTEAHKTNKPCGKCYFYLLISKTFVEAGINNSKKKRNIQKKNELMFANAEEE
          ..VPPQ.AL.M.QQLQKELTEAHKT.KPC.KCYFYLLIS.TFVEAG.NNS.KK..IQKKNELMFANAEEE
Retrocopy SSVPPQVALSMYQQLQKELTEAHKTSKPCEKCYFYLLISRTFVEAGKNNSEKKCYIQKKNELMFANAEEE

Parental  FFCXK
          FF..K
Retrocopy FFYGK

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_1260 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1260 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 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012873	1 retrocopy	retro_cfam_1356,
Callithrix jacchus	ENSCJAG00000012411	1 retrocopy	retro_cjac_2838,
Dasypus novemcinctus	ENSDNOG00000002939	1 retrocopy	retro_dnov_530,
Macaca mulatta	ENSMMUG00000008541	1 retrocopy	retro_mmul_472,
Oryctolagus cuniculus	ENSOCUG00000008761	1 retrocopy	retro_ocun_843,
Otolemur garnettii	ENSOGAG00000010901	1 retrocopy	retro_ogar_1184,
Ictidomys tridecemlineatus	ENSSTOG00000011828	4 retrocopies	retro_itri_1004, retro_itri_1130, retro_itri_1513, retro_itri_559,
Tupaia belangeri	ENSTBEG00000002570	4 retrocopies	retro_tbel_1259, retro_tbel_1260 , retro_tbel_2963, retro_tbel_3044,