Sequence
atgc intronic sequence ATGC exonic sequence...aataggaattaaaattaagtgtcagggaaaacagggttgggtttggctttattaacgtatgttgagtgggggatttttttttgggtatggaaatttgaagGGCAATGTTGGGAAGCGGGGGGGTTTCAGACGGGTACGAGGTTGGCTCAAAGAGACAAAGAATGATGGAATCCAATCCATACTTCGCAGTGAGCAGCGGA
Basic information
species | Glycine max |
transcript | GLYMA09G33090.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G33090.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g03710.1 (Oryza sativa), 3'ss of exon 1
aataggaattaaaattaagtgtcagggaaaacagggttgggtttggctttattaacgtatgttgagtgggggatttttttttgggtatggaaatttgaagGGCAATGTTGGGAAGCGGGGGGGTTTCAGACGGGTACGAGGTTGGCTCAAAGAGACAAAGAATGATGGAATC---CAATCCATACTTCGCAG---TGAGCAGCGGA--------------
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--------------tggattatctgaagggcaatgatgggaggcgggggggtt----tcggatgggtacgagggatcaaagaggccacgaatgatcgaatc-caat-ccatacttcgcagTGACCGCAGGCAGTCCCTTGGATGTCTCAAAGAGGGCCAGGATGATGGAACCAGCCCCTCCCTATTTCGGAGCCATGGGCAGCAGCGCTGCTGGTGGCAC
upper sequence: GLYMA09G33090.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g03890.1 (Oryza sativa), 3'ss of exon 1
aataggaattaaaattaagtgtcagggaaaacagggttgggtttggctttattaacgtatgttgagtgggggatttttttttggg--tatggaa-atttgaagGGCAATGTTGGGAAGCGGGGGGGTTTCAGACGGGTACGAGGTTGGCTCAAAGAGACAAAGAATGATGGAATCCAATCCATACTTCGCAGTGAGCAGCGGA---
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---ttatgtttgggttattttatatgaaatggggattgagagatgaggggatcgtctccttttttttttcttttctctttttgggactctggattatctgaagGGCAATGATGGGAGGCGGGGGGGTTTCGGATGGGTACGAGG---GATCAAAGAGGCCACGAATGATCGAATCCAATCCATACTTCGCAGTGACCGCAGGCAGT
upper sequence: GLYMA09G33090.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G66010.1 (Arabidopsis thaliana), 3'ss of exon 1
aataggaattaaaattaagtgtcagggaaaacagggttgggtttggctttattaacgtatgttgagt-gggggatttttttttgggtatg------gaaatttgaagGGCAATGTTGGGAAGCGGGGGGGTTTCAGACGGGTACGAGGTTGGCTCAAAGAGACAAAGAATGATGGAATCCAATCCATACTTCGCAGTGAGCAGCGGA------------
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-atatagactaagaatga----cagggaagtctgggttgggtgtggttatattaact--ggttgagttgggggatctttttccgggtttcttgtttggtaattgaagGGCCATGTTTGGGAGCGGGGGG------------TACGAGGTGGGATCAAAGAGACAAAGAATGATGCAATCAAATCCCTACTTGGCAGTTGGCACTGGACCTACCAGCTTT
upper sequence: GLYMA09G33090.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G66010.2 (Arabidopsis thaliana), 3'ss of exon 1
---------aataggaattaaaattaagtgtcagggaaaacagggttgggtttggctttattaacgtatgttgagtgggggatttttttttgggtatggaaatttgaagGGCAATGTTGGGAAGCGGGGGGGTTTCAGACGGGTACGAGGTTGGCTCAAAGAGACAAAGAATGATGGAATCCAATCCATACTTCGCAGTGAGCAGCGGA
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ggtttcttgtttggtaattgaagggccatgtttgggagcggggggtacgaggtgggatca--aagagacaaagaatgatgcaatcaaatccctacttggcagTT---GGCACTGGACCTACCAGCTTTCCACCTTTTGGCTATGCCG--GCGGATTCCCAGTCGTTCGCCTCAGGGGTCTTCCCTTCA-ACTGCGCTGACATTGACAT-
upper sequence: GLYMA09G33090.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0044g00080.t01 (Vitis vinifera), 3'ss of exon 1
aataggaattaaaattaagtgtcagggaaaacagggttgggtttggctttattaacgtatgttgagtgggggatttttttt------tgggtatggaaatttgaagGGCAATGTTGGGAAGCGGGGGGGTTTCAGACGGGTACGAGGTTGGCTCAAAGAGACAAAGAATGATGGAATCCAATCCATACTTCGCAGTGAGCAGCGGA
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aataaagac----attaggtgtcaggaaaacgtgggttgggtttggttttattaac--aggttgagtgggggattttttttctgttttgggtatggataattgaagGGCAATGTTGGGAAGCGGGGGGGTTTCGGACGGGTACGAGATCGGCTCAAAGAGACAAAGAATGATGGAATCAAATCCCTACTTCGCAGTGAGCAGCAGTMapped 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|207814608|gb|GD788517.1|GD788517EST: CCTTTTGCTCGGTCCTTCGCTGAACACGGAAGCATGTACGGTCCCCGAGG GGCAATGTTGGGAAGC-GGGGGGTTTCAGACGGGTTACGTAGGTTGGCTCA
genomic: CCTTTTGCTCGGTCCTTCGCTGAACACGGAAGCATGTACGGTCCCCGAGGgtatgtcgac ... aaatttgaagGGCAATGTTGGGAAGCGGGGGGGTTTCAGACGGG-TACG-AGGTTGGCTCA
EST:
gi|298169487|gb|HO020847.1|HO020847EST: CCTTTTGCTCGGTCCTTCGCTGAACACGGAAGCATGTACGGTCCCCGAGG GGCAATGTTGGGAAGCNNNNNNNTTTCAGACGGGTACGAGGTTGGCTCAAA
genomic: CCTTTTGCTCGGTCCTTCGCTGAACACGGAAGCATGTACGGTCCCCGAGGgtatgtcgac ... aaatttgaagGGCAATGTTGGGAAGCGGGGGGGTTTCAGACGGGTACGAGGTTGGCTCAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctttattaacgtatgttgagtgggggatttttttttgggtatggaaatttgaagGGCAATGTTGGGAAGCGGGGGGGTTTCAGACGGGTACGAGGTTGGCTCAAAGAGACAAAGAATGATGGAATCCAATCCATACTTCGCAGTGAGCAGCGGA
tattaac putative branch site (score: 1)
attttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aataggaattaaaattaagtgtcagggaaaacagggttgggtttggctttattaacgtatgttgagtgggggatttttttttgggtatggaaatttgaagGGCAATGTTGGGAAGCGGGGGGGTTTCAGACGGGTACGAGGTTGGCTCAAAGAGACAAAGAATGATGGAATCCAATCCATACTTCGCAGTGAGCAGCGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - aaaattaa
- - - - - - - - - - - - -ggaaaac
- - - - - - - - - - - - - - - - -gggttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggtatg