Sequence
atgc intronic sequence ATGC exonic sequence...ttcttctttcctaattactcggtttaatgtggacctatgatcactgcaattttatataaatagaatttgtccttaaatttgatatgcaatctaatttcagTGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAG
Basic information
species | Glycine max |
transcript | GLYMA02G47270.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 11
-ttc--ttctttcctaattactcggtttaatgtggacctatgatcactgcaattttatataaataga-atttgtccttaaatttgatatgcaatctaatttcagTGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAG
||| || || ||| | || ||| ||| | || || || |||||||| | | | | | || | | | |||| || |||||| ||||||||||| ||||| | || |||||||| |||||||| || |||||||| ||||||||||| |||||||| |||||||| |||||
attcaatttcttgttaaagattctgtt-aataaagctcttcatacatcc---ttgagtataaatacataactattgtcaattatttcttacaattgctttccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGTAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGAGAAGGAGACAATGGCAAACAG
upper sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
ttcttctttcctaattactcggtttaatgtggacctatgatcactgcaattttatataaatagaatttgtcc--ttaaatttgatatgcaatctaatttcagTGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAG
||| ||||| | | || | | | |||| | | |||| ||| | || | |||| | | | ||||| | | |||||| ||||||||||| ||||| | || ||||||||||||||||| || |||||||| ||||||||||| || ||||| |||||||| |||||
ggattcattccttgtcaagtatcttgttagtaaagcac-atca-taaatttttgaatagaaaggcataactatgttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG
upper sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 10
ttcttctttcctaattactcggtttaatgtggacctatgatcactgcaattttatataaatagaatttgtccttaaatttgatatgc---aatctaatttcagTGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAG
| | | |||| | | | || | | | | || | | | || | |||| ||| || || |||||| || |||||||| ||||| ||||| |||||||| |||||||| ||||||||||| |||||||||||| | |||||||||||||| ||||||
---aacatgcacaattgacccctcatgcactagaattcaattcatcagtcatcacaagaacatctatgtactctacaaatgatttgctacaactggtttccagTGGCGAAAGTATGGAGAATGCACTACGTGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGTGACAATGGACAACAG
upper sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 12
ttcttctttcctaatt-actcggtttaatgtggacctatgatcactgcaatt-ttatataaatagaatttgtccttaaatttgatatgcaatctaatttcagTGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAG
||| | |||| | | | | | | ||||||| | | || || ||||| | | | | ||||| || ||| || |||||| || || ||||| ||||| ||||||||||||| |||||||| ||||||||||| |||||||||||| | ||||| |||||||| ||||||
ttcatgcactagaattcaattcatcacaagaacatgtatgatcccccctatccttgaataaagtgtactctgcaaatgatttgcta--caactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG
upper sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 11
ttcttctttcctaattactcggtttaatgtggacctatgatcactgcaattttatataaatagaatttgtccttaaatttgatatgcaatctaatttcagTGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAG
|| | |||| || ||| || | | || | |||| | ||| | || || ||||||||||| || ||||| |||||||||||||||| ||||| |||||||| ||||| |||||||||||||| |||||||||||||||
----------------------------gtaaa---gaaatcagcttaaacactaatagttaacgtcaatactatataatgattttgtctctgaacatagCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG
upper sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 11
lower sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 11
ttcttctttcctaattactcggtttaatgtggacc-tatgatcactgcaattttatataaatagaatttgtccttaaatttgata----tgcaatctaatttcagTGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAG
| |||||||| | | | |||| | | || || || | | || | | | || | | | || ||||| | | |||| ||||| ||||| ||||| ||||| |||||||||| ||||||||||||||||| ||||| || || ||||| ||||||||||||||||||||||||
--gtactttcctatatcttagctttagtttatacaataggaacttccccatcct-ttcatatcccactctctcaccaacttgatggtgttttgaaataatgctagTGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAG
upper sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 11
--------ttcttctttcctaattactcggtttaatgtggacctatgatcactgcaattttatataaatagaatttgtccttaaatttgatatgcaatctaatttcagTGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAG
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aaaggaaaaagaagtgcaaaaagcatattcctggttatggacccattttctctttgtcttt-------tgcattttggtttgaaccatcttctctta-ctgatgccagTGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGMapped 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|298180251|gb|HO025466.1|HO025466EST: AGTGGTGTGGATTTCTGCAAGAGGTTGTGTGGTGTCTCTATCATCCGGAG TGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGAT
genomic: AGTGGTGTGGATTTCTGCAAGAGGTTGTGTGGTGTCTCTATCATCCGGAGgtatcgtttt ... ctaatttcagTGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaattttatataaatagaatttgtccttaaatttgatatgcaatctaatttcagTGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAG
atctaat putative branch site (score: 3)
tttatataaatagaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcttctttcctaattactcggtttaatgtggacctatgatcactgcaattttatataaatagaatttgtccttaaatttgatatgcaatctaatttcagTGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAG
- - - - - - - - - - - - - - - - -cctatga
- - - - - - - - - - - - - - - - - - - - -cactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgcaa