RetrogeneDB ID: retro_tbel_613

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_2544:577997..578547(-)
• Located in intron of: ENSTBEG00000005393

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAP1B
• Ensembl ID: ENSTBEG00000013380
• Aliases: None
• Description: RAP1B, member of RAS oncogene family [Source:HGNC Symbol;Acc:9857]

Sequence

>retro_tbel_613
ATGCATGAGTACAAGCTAGTGTTCCTTGGTTCAGGAGCCGTGGGGACATCTGCTCTGACAGTTGCGTTTGTTCAGGGAAC
TTTTGTTGAAAAATATGACCCAATCATAGAAGATTCCTTCAGAAAGCAAGCTGAAGTAGATTGCCAACAGTGTGCACTCA
AAATCCTGGATACAACAGGGACAGAACAACTTACGGCAGTGAGGGATTTGTATATGAAGAATGGCCAAGGGTTTGCGCTA
GTGTGTTACATTACAGCGCAGTCCACGTTTAGTGACTTATAGGACCTGAGAGAACACATTTTATGAGTTAAGGGCACAGA
AGATGTTCCAGTGATTTTGGTTGGCAAGAAATGTGACCTGGAAGATGAGCAAGTAGTTGGCAAAGAACAGCACCAGACTT
GAGCAAGACAGTGCGTAACTGTGCCTTTTTAGACTCCTCTGCAAAATCAAAGATCAACGTTAATGAGGTATTTTATGACC
TGGTCAGACAGATAAAGAGAAAAACACCAGTGTAAAGAAGAGGCCTAAAAAAAATTCATGTCGGCTGCTC

Alignment

ORF - retro_tbel_613 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.34 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDL
          M.EYKLV.LGSG.VG.SALTV.FVQG.FVEKYDP.IEDS.RKQ.EVD.QQC.L.ILDT.GTEQ.TA.RDL
Retrocopy MHEYKLVFLGSGAVGTSALTVAFVQGTFVEKYDPIIEDSFRKQAEVDCQQCALKILDTTGTEQLTAVRDL

Parental  YMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQW-N
          YMKNGQGFALV..ITAQSTF.DL.DLRE.IL.VK.T.DVP.ILVG.KCDLEDE.VVGKEQ.Q..ARQ...
Retrocopy YMKNGQGFALVCYITAQSTFSDL*DLREHIL*VKGTEDVPVILVGKKCDLEDEQVVGKEQHQT*ARQC<R

Parental  NCAFLESSAKSKINVNEIFYDLVRQINRKTPV-PGKARKKSSCQLL
          NCAFL.SSAKSKINVNE.FYDLVRQI.RKTPV...K.....SC.LL
Retrocopy NCAFLDSSAKSKINVNEVFYDLVRQIKRKTPV<VKKRPXXXSCRLL

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_613 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_613 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 12 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008637	1 retrocopy	retro_amel_103,
Callithrix jacchus	ENSCJAG00000007261	3 retrocopies	retro_cjac_1435, retro_cjac_2371, retro_cjac_607,
Cavia porcellus	ENSCPOG00000008272	4 retrocopies	retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Gorilla gorilla	ENSGGOG00000025649	1 retrocopy	retro_ggor_2836,
Loxodonta africana	ENSLAFG00000016460	1 retrocopy	retro_lafr_482,
Mus musculus	ENSMUSG00000052681	1 retrocopy	retro_mmus_1370,
Nomascus leucogenys	ENSNLEG00000003573	2 retrocopies	retro_nleu_1034, retro_nleu_481,
Otolemur garnettii	ENSOGAG00000005746	2 retrocopies	retro_ogar_2260, retro_ogar_272,
Sarcophilus harrisii	ENSSHAG00000011497	1 retrocopy	retro_shar_425,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,
Tupaia belangeri	ENSTBEG00000003830	2 retrocopies	retro_tbel_2242, retro_tbel_271,
Tupaia belangeri	ENSTBEG00000013380	4 retrocopies	retro_tbel_2145, retro_tbel_4650, retro_tbel_4658, retro_tbel_613 ,