RetrogeneDB ID: retro_tbel_3836

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_1991:28903..29901(+)
• 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_3836
TGGAACTGCCCCCTCCTGATGCAAGCGTGGAAACTGGGCCCAGCCTTGGCGACTGGAAATGTGGTGTGATGAAAGTAGCT
GAGCAGATGCCCCTCACCGCCCTGCTTGTGACCAACTTGATCAAGGAGTCTGACTCTCCCCCGGCATGGTCAATATTGTT
CCTGGATTTGGGCCCTACTGTCGGGGCTGCCATCGCCTACCATGAGGATGTGAACAAGGTGGCATTCACAGGCTCCACTG
AGGTCGGCCACCTTCTCCAGGTTGCTGCAGGGAAGAGTAATTTCAAGAGGGTGACGCTGGAGCTGGGGGGCCAAGAGCCC
CAACATCATCATGTCAGACGCTGACATGGCCTGGGCTGTAGGAGCAGGCCCACTTCACCCTGTTCTTCAATCAAGGGCCA
GTGTTGTTGTGCAGGCTCTCAGACCTATGTGCAGGAGGCCATGTATGCCAAGTTCGTAGAGAGGAGCACAGACCAGGACA
AGTTGCGGGTGGTCGGGAAACCCTTTGACAGCCAGACCAAGCAGGGGCCCCAGGGAGATGAAACTCAGTTTAAAAATATC
CTTGGCTACATCCAATCTGGGAAGCAAGAGGTGACGAAGCTGCTGTGTGGTGGGGTCCTCCTCCTGACTGTAGTGTCTTC
ATCAAGCCCACTGTGTCTGGAGATGTTCAAGATGGCATGACCATGGCCAAGGAGGAGATCTTTGGGCCAGTGATGCAGAT
CCTGAAGTTCAAAACCATAGAGGAGGTTGTCAGGAGAGCCAACAATTCCAAATATGGGCTGACTGCAGCTATCTTCACCA
AGGACTTGGACAATGTCAATTATCTGTCCCAAGTCCTCCAGGCTGGCACTGTGTGGGTCAACTGCTATGATGTGTTTGGT
GCCCAGTCACCGTTTGGCGGCTACCAGACGTGAGGCAGTGGCCGGAAGCTGGGGGAGTACCTCTGCAGGCGTACACTGAA
GTGAAGACGTCACAGTCAAAGTTCCTCAGAAGAACTCG

Alignment

ORF - retro_tbel_3836 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.09 %
• Parental protein coverage: 66.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  WNFPLVMLIWKIGPALSCGNTV-VVKPAEQTPLTALHVASLIKEAGFPP-GVVNIVPGY-GPTAXXXXXX
          WN.PL.M..WK.GPAL..GN.V.V.K.AEQ.PLTAL.V..LIKE...PP.G.VNIVPG..GPT.......
Retrocopy WNCPLLMQAWKLGPALATGNVV<VMKVAEQMPLTALLVTNLIKESDSPP<GMVNIVPGF>GPTVGAAIAY

Parental  XXXXXXXXXXXXXXVGKMIKEAAGKSNLKRVTLELGG-KSPCIVFADADLDNAV-EFAHHGLFYHQG-QC
          ..............VG.....AAGKSN.KRVTLELGG.KSP.I...DAD...AV.E.AH..LF..QG.QC
Retrocopy HEDVNKVAFTGSTEVGHLLQVAAGKSNFKRVTLELGG>KSPNIIMSDADMAWAV>EQAHFTLFFNQG>QC

Parental  CIAASRLFVEESIYDEFVRRSVERAKKYVLGNPLTPGVNQGPQIDKEQHDKILDLIESGKKEGAKLECGG
          C.A.S...V.E..Y..FV.RS....K..V.G.P......QGPQ.D..Q...IL..I.SGK.E..KL.CGG
Retrocopy CCAGSQTYVQEAMYAKFVERSTDQDKLRVVGKPFDSQTKQGPQGDETQFKNILGYIQSGKQEVTKLLCGG

Parental  -GPWGNKGYFIQPTVFSNVTDEMRIAKEEIFGPVQQIMKFKSLDDVIKRANNTSYGLSAGIFTKDIDKAV
          .GP......FI.PTV...V.D.M..AKEEIFGPV.QI.KFK....V..RANN..YGL.A.IFTKD.D...
Retrocopy <GPPPDCSVFIKPTVSGDVQDGMTMAKEEIFGPVMQILKFKTIEEVVRRANNSKYGLTAAIFTKDLDNVN

Parental  TVSSALQAGTVWVNCYSVVTAQCPFGGFKMSGNGRELGEY-GFHEYVEVKT-VTMKISQKNS
          ..S..LQAGTVWVNCY.V..AQ.PFGG....G.GR.LGEY.....Y.EVKT.VT.K..QKNS
Retrocopy YLSQVLQAGTVWVNCYDVFGAQSPFGGYQT*GSGRKLGEY<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_3836 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3836 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,