RetrogeneDB ID: retro_tbel_2156

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_102710:2567..3565(-)
• 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_2156
TGGAACACCCTCCTCCTGATGCAAGCGTGGAAACTGGGCCCAGCCATGGCGACTGGAAATGTGGTTTTGATGAATGTAGC
TGAGCAGACGCCCCTCACTGCCCTGTATGGGGCCAACCTGATCAAGGAGGCTGGCTTTACCCCGGCATGGTTAATATTGT
TCCTGGATTTGGTCCTACTGTCGGGGCTGCCATCGCCTACCATGAGGATGTGAACAAGGTGGCATTCACAGGCTCCACTG
AGGTTGGCCACCTTCTCCAGGTTGCTGCCGGGAAGAGTAATCTCAAGAGGGTGACGCTGGAGCTGGGGGGCCAAGAGCCC
CAACATCATCATGTCAGACGCTGACATGGCCTGGGCTGTGGAGCAGGGCCACTTCACCCTGTTCTTCAATCAAGGGCCAG
TGTTGTTGTGCAGGCTCTCGGACCTATGTGCAGGAGGCCATGTATACCAAGTTCATAGAGTGGAGCATGGCTCGGGCCAA
TTTGCGGGTGGTCGGGAACCCCTTTGACAGCCAGACCAAGCAGCGGCCCCAGGGAGATTAAACTCAGTTTAAAAAGATCC
TTGGCTATATCCAATCTGGGAAGCAAGAGGTGACGAAGCTGCTGTGTGGTGGGGGCCCTGCTCCTGAACATAGTGTCTTC
ATCAAGCCCACTGTGTTTGGAGATGTGCAAGATGGCATAACCATGGCCAAGGAGGAGATCTTTGGGCCAGTGATGCAGAT
CCTGAAGTTCAAGACCATAGAGGAGGTTGCCGGGAGAGCCCACAATTCCAAGTATGGGCTGGCTGCAGCTATCTTCACCA
ATGACGTGGACAAGGCCAATTATCTGTCCCAAGTCCTCCAGGCTGGCACTGTGTGGGATACCTGCTATGATATGTTTGGC
GCCCAGTCACCGTTTGGCGGCTACCAGACGTTGGGCAGTGGCCGGAAGCTGGGGGAGTACCGCTGCAGGCGTACACTGAA
GTGAAGACGTCACAGTCAAAGTTCCTCAGAAGAACTCG

Alignment

ORF - retro_tbel_2156 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.85 %
• Parental protein coverage: 66.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  WNFPLVMLIWKIGPALSCGNTVVVKPAEQTPLTALHVASLIKEAGFPP-GVVNIVPGYGPTAXXXXXXXX
          WN..L.M..WK.GPA...GN.V....AEQTPLTAL..A.LIKEAGF.P.G.VNIVPG.GPT.........
Retrocopy WNTLLLMQAWKLGPAMATGNVVLMNVAEQTPLTALYGANLIKEAGFTP<GMVNIVPGFGPTVGAAIAYHE

Parental  XXXXXXXXXXXXVGKMIKEAAGKSNLKRVTLELGG-KSPCIVFADADLDNAVEFAHHGLFYHQG-QCCIA
          ............VG.....AAGKSNLKRVTLELGG.KSP.I...DAD...AVE..H..LF..QG.QCC.A
Retrocopy DVNKVAFTGSTEVGHLLQVAAGKSNLKRVTLELGG>KSPNIIMSDADMAWAVEQGHFTLFFNQG>QCCCA

Parental  ASRLFVEESIYDEFVRRSVERAKKYVLGNPLTPGVNQGPQIDKEQHDKILDLIESGKKEGAKLECGGGPW
          .SR..V.E..Y..F...S..RA...V.GNP......Q.PQ.D..Q..KIL..I.SGK.E..KL.CGGGP.
Retrocopy GSRTYVQEAMYTKFIEWSMARANLRVVGNPFDSQTKQRPQGD*TQFKKILGYIQSGKQEVTKLLCGGGPA

Parental  GNKGYFIQPTVFSNVTDEMRIAKEEIFGPVQQIMKFKSLDDVIKRANNTSYGLSAGIFTKDIDKAVTVSS
          .....FI.PTVF..V.D....AKEEIFGPV.QI.KFK....V..RA.N..YGL.A.IFT.D.DKA...S.
Retrocopy PEHSVFIKPTVFGDVQDGITMAKEEIFGPVMQILKFKTIEEVAGRAHNSKYGLAAAIFTNDVDKANYLSQ

Parental  ALQAGTVWVNCYSVVTAQCPFGGFKMSGNGRELGEY-GFHEYVEVKT-VTMKISQKNS
          .LQAGTVW..CY....AQ.PFGG....G.GR.LGEY.....Y.EVKT.VT.K..QKNS
Retrocopy VLQAGTVWDTCYDMFGAQSPFGGYQTLGSGRKLGEY<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_2156 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2156 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,