Sequence
atgc intronic sequence ATGC exonic sequence...ataaatattaattgttagcattattatttttgtaagttgaaaattcgaactgcaatcttttttcctttatcactaaactaaccttatatttttttggcagTTTGTTCAAGGAATGTCCACACCCGGATGATAAGCAGAGACTGAAACTGAGCCATGAATTGGGTCTTAAACCGCGCCAGGTCAAGTTCTGGTTCCAGAAC
Basic information
species | Glycine max |
transcript | GLYMA09G34070.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G34070.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g42490.1 (Oryza sativa), 3'ss of exon 3
----------------------ataaatattaattgttagcattattatttttgtaagttgaaaattcgaactgcaatcttttt--tcctttatcactaa--actaac---cttatatttttttg-gcagTTTGTTCAAGGAATGTCCACACCCGGATGATAAGCAGAGACTGAAACTGAGCCATGAATTGGGTCTTAAACCGCGCCAGGTCAAGTTCTGGTTCCAGAAC
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gtacggttttcatctccatcttcttcttcctcttcaatgccattgccagccgtttcgatcgattcgtctccattaaaccttgctgatattgtgatactgacaagtggcgtgcatgcatccatccatgcagGCTGTTCAAGGAGTGCCCGCATCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAACTGGGCCTCAAACCTCGCCAGGTCAAGTTCTGGTTCCAGAAT
upper sequence: GLYMA09G34070.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G123140_T04 (Zea mays), 3'ss of exon 2
-----------------------------ataaatattaattgttagcattattatttttgtaagttgaaaattcgaactgcaatcttttttcctttatcactaa-----actaaccttatatttttttggcagTTTGTTCAAGGAATGTCCACACCCGGATGATAAGCAGAGACTGAAACTGAGCCATGAATTGGGTCTTAAACCGCGCCAGGTCAAGTTCTGGTTCCAGAAC
| |||| | | || || || | || || || || || | | | | | || | | | | | | ||| |||||||||| || || |||||||| || |||||| | ||||| |||||||| || |||| || ||||| |||||||||||||||||||||||||||
gtaagacacacacatatatacgcttgccttttcatatataataataatcttctt-ctccgatatattataatctcttacggatgcatgcatggcaatggcaatggccggcattgcacggacgacatacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAGCTGGGGCTCAAACCCCGCCAGGTCAAGTTCTGGTTCCAGAAC
upper sequence: GLYMA09G34070.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0012g02030.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------ataaatattaattgttagc----attattatttttgtaagttgaaaattcgaactgcaatcttttttc-ctttatcactaaactaaccttatatttttttggcagTTTGTTCAAGGAATGTCCACACCCGGATGATAAGCAGAGACTGAAACTGAGCCATGAATTGGGTCTTAAACCGCGCCAGGTCAAGTTCTGGTTCCAGAAC
| ||| || | | | || | | | | || || | | | || || | | | | || | | | | ||||| ||||||| ||||||||||| |||||||| ||||| |||||||| ||||||| ||||| ||| | || || ||||| ||||| |||||||| |||||||| |||
gtatgctactatttctctctcactctcttcaaaaacatggttcttatacttcaatcacaacccattacgcataaatgttgggaaaatcacctaaactcacactctagttgcaccaccgtcactcattttttgcagTTTATTCAAGGAATGCCCACACCCAGATGACAAGCAGAGGATGAAACTCAGCCAAGAACTTGGCCTCAAACCACGCCAAGTCAAGTTTTGGTTCCAAAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgaactgcaatcttttttcctttatcactaaactaaccttatatttttttggcagTTTGTTCAAGGAATGTCCACACCCGGATGATAAGCAGAGACTGAAACTGAGCCATGAATTGGGTCTTAAACCGCGCCAGGTCAAGTTCTGGTTCCAGAAC
aactaac putative branch site (score: 1)
ccttatattttttt CT-rich tract
taaactaaccttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataaatattaattgttagcattattatttttgtaagttgaaaattcgaactgcaatcttttttcctttatcactaaactaaccttatatttttttggcagTTTGTTCAAGGAATGTCCACACCCGGATGATAAGCAGAGACTGAAACTGAGCCATGAATTGGGTCTTAAACCGCGCCAGGTCAAGTTCTGGTTCCAGAAC
- - - - - - - - - - - - - - - - - - - - - - - -aactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actaacc