RetrogeneDB ID: retro_tbel_3843

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_23084:2..967(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ALDH1A1
• Ensembl ID: ENSTBEG00000001455
• Aliases: None
• Description: aldehyde dehydrogenase 1 family, member A1 [Source:HGNC Symbol;Acc:402]

Sequence

>retro_tbel_3843
GGGCCCAGCCTTGGTGACTGGAAATGTGGCGTTAAGATGAAAGTAGTTGAGCAGACGCTCCTCACTGCCCTGTATGGGGC
CAACCTGATCAAGGAGGCCGGCTTTACCCCGGCATGGTTAATATTGTTCCTGGATTTGGTCCTACTGTCGGGGCTGCTAT
CACCTCCCATGAGGATGTGGACAAGGTGGCATTCACAGGCTCCACTGAGGTCGGCCACCTTCCCCAGGTTGCTGCAGGGA
AGAGTAATCTCAAGAGGGTGATGCTGGAGCTGGGGGGCAAGAGCCCCAACATCATCATGTCAGATGCTGACATGGCCTGG
GCTGTGGAGCAGGGCCACTTCACCCTGTTCTTCAATCAAGGGCCAGTGTTGTTGTGCAGGCTCTCAGACCTATGTGTAGG
AGGCCATGTAGGCCGAGTTCGTGGAGCGGAGCATAGCCCGGGCCAAGATATGGGTGGTCGGGAACCCCTTTGACAGCCAG
ACCAAGCACGGGCCCCAGGAAGATGAAACTCAGTTTAAAAATATCCTTGGCTACATCCAATCTGGGAAGCAAGAGGTGAC
GAAGCTGCTGTGTGGTAGGGGGGCCTGCTCCTGACCATAGTGTCTTCATCCAGCCCACTGTGTTTGGAGATGTGCAAGAT
GGCATAACCATGGCCAAGGAGGAGATCTTTGGGCCAGTGATGCAGATCCTGAAGTTCAAGACCACAGAGGAGGTTGTCAG
GAGAGCGAACGATTCCAAATATGGGCTGGCTGCAGCTATCTTCACCAAGGACTTGGACAAGGCCAATTATCTGTCCCAAG
TCCTCCAGGCAGGCACTGTGTAGGTCAACTGCTATGATGTGTTTGGCGCCCAGTCACCGTTTGGCGGTAACCAGACGTCA
GGCAGTGGCCAGAAGCTGGGGGAGTACCTCTGCAGGCGTACACTGAAGTGAAGACGTCACAGTCAAAGTTCCTCAGAAGA
ACTCG

Alignment

ORF - retro_tbel_3843 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.41 %
• Parental protein coverage: 64.07 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GPALS---CGNTVVVKPAEQTPLTALHVASLIKEAGFPP-GVVNIVPGYGPTAXXXXXXXXXXXXXXXXX
          GP.L....CG..V..K..EQT.LTAL..A.LIKEAGF.P.G.VNIVPG.GPT..................
Retrocopy GPSLGDWKCG--VKMKVVEQTLLTALYGANLIKEAGFTP<GMVNIVPGFGPTVGAAITSHEDVDKVAFTG

Parental  XXXVGKMIKEAAGKSNLKRVTLELGGKSPCIVFADADLDNAVEFAHHGLFYHQG-QCCIAASRLFVEESI
          ...VG.....AAGKSNLKRV.LELGGKSP.I...DAD...AVE..H..LF..QG.QCC.A.S...V.E..
Retrocopy STEVGHLPQVAAGKSNLKRVMLELGGKSPNIIMSDADMAWAVEQGHFTLFFNQG>QCCCAGSQTYV*EAM

Parental  YDEFVRRSVERAKKYVLGNPLTPGVNQGPQIDKEQHDKILDLIESGKKEGAKLECG-GGPWGNKGYFIQP
          ..EFV.RS..RAK..V.GNP.......GPQ.D..Q...IL..I.SGK.E..KL.CG.GGP......FIQP
Retrocopy *AEFVERSIARAKIWVVGNPFDSQTKHGPQEDETQFKNILGYIQSGKQEVTKLLCG>GGPAPDHSVFIQP

Parental  TVFSNVTDEMRIAKEEIFGPVQQIMKFKSLDDVIKRANNTSYGLSAGIFTKDIDKAVTVSSALQAGTVWV
          TVF..V.D....AKEEIFGPV.QI.KFK....V..RAN...YGL.A.IFTKD.DKA...S..LQAGTV.V
Retrocopy TVFGDVQDGITMAKEEIFGPVMQILKFKTTEEVVRRANDSKYGLAAAIFTKDLDKANYLSQVLQAGTV*V

Parental  NCYSVVTAQCPFGGFKMSGNGRELGEY-GFHEYVEVKT-VTMKISQKNS
          NCY.V..AQ.PFGG...SG.G..LGEY.....Y.EVKT.VT.K..QKNS
Retrocopy NCYDVFGAQSPFGGNQTSGSGQKLGEY<PLQAYTEVKT<VTVKVPQKNS

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_3843 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3843 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 3 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000031532	1 retrocopy	retro_lafr_1162,
Macropus eugenii	ENSMEUG00000008847	1 retrocopy	retro_meug_354,
Tupaia belangeri	ENSTBEG00000001455	7 retrocopies	retro_tbel_2156, retro_tbel_2326, retro_tbel_3836, retro_tbel_3843 , retro_tbel_3945, retro_tbel_3951, retro_tbel_4329,