RetrogeneDB ID: retro_tbel_2326

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_109083:3476..4402(+)
• 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_2326
TGGAACTCCCCCTCCTGATGCAAGCGTGGAAACTGGGCCCAGCCTTGGTGACTGGAAATGTGGTTGTGATGAAAGTACCT
GAGCAGACGCCCCTCACTGCCCTGTGTGGGGCCAACCTGATCAAGGAGGCCGGCTTTACCCCAGCATGGTTAATATTGTT
CCTGGATTTGGGCCTACTGTCGGGGCTGCCATCGCCTACCATGAGGATGTGAACAAGGTGGCATTCACAGGCTCCACTGA
GGTTGGCCACCTTCTCCAGGTTGCTGAAGGGAAGAGTAATCTCAAGAGGGTGACGCTGGAGCTGGGGGGCCAAGAGCCCC
AACATCATCATGTCAGACGCTGACATGGCCTGGGCTGTGGAGCAGGCCCATTTAGCCCTGTTCTTCAATCAAGGGCCAGT
GTTGCTGTGTAGGCTCTCGGACCTATGTGCAGGAGGCCATGTATGCCAAGTTCGTAGAGAGGAGCACAGCCCAGGACAAG
TTGCGGGTGGTCGGGAACCCCTTTGACAGCCAGACAAAGCAGGGGCCCCAGGGAGATGAAACTCAGTTTAAAAAGATCCT
TGGCTACATCCCATCTGGGAAGCAAGAGGTGACGAAGCTGCTGTGTGGTGGGGGCCTGCTCCTGACTGTAGTGTCTTCAT
CCAGCCCACTGTGTTTGGAGAGGTTCAAGATGGCATGACCATGGCCAAGGAGGAGATCTTTGGGCCAGTGATGCAGATCC
TGAAGTTCAAGACCATAGAGGAGGTTGTCAGGAGAGCCAACAATTCCAAATATGGGCTGACTGCAGCTATCTTCACCAAG
GACTTGGACAATGTCAATTATCTGTCCCAAGTCCTCCAGGCTGGCACTGTGTGGGTCAACTGCTATGATGTGTTTGGTGC
CCAGTCACCGTTTGGCGGCTACCAGACGTGAGGCAGTGGCCGGAAG

Alignment

ORF - retro_tbel_2326 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.41 %
• Parental protein coverage: 61.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  WN-FPLVMLIWKIGPALSCGNTVVVKPAEQTPLTALHVASLIKEAGFPPG-VVNIVPGYGPTAXXXXXXX
          WN..PL.M..WK.GPAL..GN.VV.K..EQTPLTAL..A.LIKEAGF.P...VNIVPG.GPT........
Retrocopy WN<LPLLMQAWKLGPALVTGNVVVMKVPEQTPLTALCGANLIKEAGFTPA<MVNIVPGFGPTVGAAIAYH

Parental  XXXXXXXXXXXXXVGKMIKEAAGKSNLKRVTLELGG-KSPCIVFADADLDNAVEFAHHGLFYHQG-QCCI
          .............VG.....A.GKSNLKRVTLELGG.KSP.I...DAD...AVE.AH..LF..QG.QCC.
Retrocopy EDVNKVAFTGSTEVGHLLQVAEGKSNLKRVTLELGG>KSPNIIMSDADMAWAVEQAHLALFFNQG>QCCC

Parental  AASRLFVEESIYDEFVRRSVERAKKYVLGNPLTPGVNQGPQIDKEQHDKILDLIESGKKEGAKLECGGG-
          ..SR..V.E..Y..FV.RS....K..V.GNP......QGPQ.D..Q..KIL..I.SGK.E..KL.CGGG.
Retrocopy VGSRTYVQEAMYAKFVERSTAQDKLRVVGNPFDSQTKQGPQGDETQFKKILGYIPSGKQEVTKLLCGGG<

Parental  PWGNKGYFIQPTVFSNVTDEMRIAKEEIFGPVQQIMKFKSLDDVIKRANNTSYGLSAGIFTKDIDKAVTV
          P......FIQPTVF..V.D.M..AKEEIFGPV.QI.KFK....V..RANN..YGL.A.IFTKD.D.....
Retrocopy PAPDCSVFIQPTVFGEVQDGMTMAKEEIFGPVMQILKFKTIEEVVRRANNSKYGLTAAIFTKDLDNVNYL

Parental  SSALQAGTVWVNCYSVVTAQCPFGGFKMSGNGRE
          S..LQAGTVWVNCY.V..AQ.PFGG....G.GR.
Retrocopy SQVLQAGTVWVNCYDVFGAQSPFGGYQT*GSGRK

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_2326 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2326 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,