Sequence
atgc intronic sequence ATGC exonic sequence...taactactaactagtttttcagactttgttgattgaatattgagttctgcttaagctacatgttctgttgacacccatttttaatttgcatactgtacagATCCTTGTTGCTACTCCTGGAAGGCTAAGAGATCATACTGAGAATACTGCTGGTTTTGCAACTAGGCTGATGGGTGTGAAGGTCTTGGTGCTTGATGAAG
Basic information
species | Glycine max |
transcript | GLYMA16G02880.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G02880.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G156158_T01 (Zea mays), 3'ss of exon 4
taactactaactagtttttcagactt-tgttgattgaatattgagttctgcttaagctacatgttctgttgacacccatttttaatttgcatactgtacagATCCTTGTTGCTACTCCTGGAAGGCTAAGAGATCATACTGAGAATACTGCTGGTTTTGCAACTAGGCTGATGGGTGTGAAGGTCTTGGTGCTTGATGAAG
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--gttgtatgcatgaatcacagattcacagtaatacagtgcatacatatctaggtgcaacacatgc-attaatactc-tggttcttttaaat------tagATTCTTGTTGCTACTCCTGGAAGGCTAAAGGATCATCTTGAGAACACGCCTGGATTCTCCACCCGAATTAGAGGTGTCAAGGTTCTTGTTCTAGATGAGG
upper sequence: GLYMA16G02880.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G08610.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------------------taactactaactagtttttcagactttgttgattgaatattgagttctgcttaagctac-atgttctgttgacacccatttttaa-----------tttgcatactgtacagATCCTTGTTGCTACTCCTGGAAGGCTAAGAGATCATACTGAGAATACTGCTGGTTTTGCAACTAGGCTGATGGGTGTGAAGGTCTTGGTGCTTGATGAAG
||| || | | | | || || | | || | | ||| || ||| || || | | ||| || | |||| | ||| | ||||||||||| ||||| ||||||||||| | ||| |||| ||| || ||| |||| || ||||| || ||||||||||||| ||| | |||||||| ||||
gtaataagaaatttcttccgtctctacaggtgttttaatttgaagttaattatgagcaaatcttgcacttcccttaaactgcgcttctaagatggctgcagataccgtgacctatatctatatattgttgaataatcacatatttgaacactct-cagATCCTTGTGGCTACACCTGGAAGGCTCAAAGACCATATTGAAAACACTTCTGGATTCGCAACAAGATTGATGGGTGTGAAAGTCCTTGTGCTTGACGAAG
upper sequence: GLYMA16G02880.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G08620.1 (Arabidopsis thaliana), 3'ss of exon 4
-----taactactaactagtttttcagact---ttgttgattgaatattgagttctgcttaagctacatgttctgttgacacccatttttaatttgcatactgtacagATCCTTGTTGCTACTCCTGGAAGGCTAAGAGATCATACTGAGAATACTGCTGGTTTTGCAACTAGGCTGATGGGTGTGAAGGTCTTGGTGCTTGATGAAG
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tttttgcattatttgtcttccctgcagtcaaagtggctgcagagatggtgatctttgtct---ctgtatatttt-tgaataataacat---attttcacactct-cagATTCTCGTGGCTACACCCGGAAGGCTCAAAGACCATATCGACAACACTTCTGGATTTGCAACAAGGTTGATGGGTGTGAAAGTCCTTGTGCTTGATGAAG
upper sequence: GLYMA16G02880.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0046g01010.t01 (Vitis vinifera), 3'ss of exon 5
taactactaactagtttttcagactttgttgattgaatattgagttctg-cttaagctacatgttctgttgacaccc-atttttaa--tttgcatactgtacagATCCTTGTTGCTACTCCTGGAAGGCTAAGAGATCATACTGAGAATACTGCTGGTTTTGCAACTAGGCTGATGGGTGTGAAGGTCTTGGTGCTTGATGAAG
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---atgctctgcaatctga-aaacctcaataaaagcaaattaattttcatcttgaaattgttaattgggaaatattttatttgtgggccttgtgatatttacagATTCTTGTAGCTACCCCTGGACGGCTAAAGGACCATATTGAGAATACAGCAGGATTTGCAACTCGTCTGATGGGTGTCAAAGTCCTTGTACTTGATGAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|16996982|gb|BM086354.1|BM086354EST: GGACAAGACTTGCTTTAGAGCAGAAACGGATGCAGGCAAACCCTTGCCAG ATCCTTGTTGCTACTCCTGGAAGGCTAAGAGATCATACTGAGAATACTGCT
genomic: GGACAAGACTTGCTTTAGAGCAGAAACGGATGCAGGCAAACCCTTGCCAGgtaaattctt ... tactgtacagATCCTTGTTGCTACTCCTGGAAGGCTAAGAGATCATACTGAGAATACTGCT
EST:
gi|15814026|gb|BI786301.1|BI786301EST: ACAAGACTTGCTTTAGAGCAGAAACGGATGCAGGCAAACCCTTGCCAG ATCCTTGTTGCTACTCCTGGAAGGCTAAGAGATCATACTGAGAATACTGCT
genomic: ACAAGACTTGCTTTAGAGCAGAAACGGATGCAGGCAAACCCTTGCCAGgtaaattctt ... tactgtacagATCCTTGTTGCTACTCCTGGAAGGCTAAGAGATCATACTGAGAATACTGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgcttaagctacatgttctgttgacacccatttttaatttgcatactgtacagATCCTTGTTGCTACTCCTGGAAGGCTAAGAGATCATACTGAGAATACTGCTGGTTTTGCAACTAGGCTGATGGGTGTGAAGGTCTTGGTGCTTGATGAAG
ttttaat putative branch site (score: 3)
atttttaatttgcata TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taactactaactagtttttcagactttgttgattgaatattgagttctgcttaagctacatgttctgttgacacccatttttaatttgcatactgtacagATCCTTGTTGCTACTCCTGGAAGGCTAAGAGATCATACTGAGAATACTGCTGGTTTTGCAACTAGGCTGATGGGTGTGAAGGTCTTGGTGCTTGATGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - -gactttg
- - - - - - - - - - - - - - - - - - - - - - ttctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgac