Sequence
atgc intronic sequence ATGC exonic sequence...attgttaatgattatgaatgttctaatgctagatgggcatccaatttctttatatagatctattctaaatttttcaaggtactgatgattgcattttcagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTTAGT
Basic information
species | Glycine max |
transcript | GLYMA12G33340.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G33340.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os04g28460.1 (Oryza sativa), 3'ss of exon 17
------------------attgttaatgattatgaatgttctaatgctaga-tgggcatccaatttctttatatagatctattctaaatttttcaaggtactgatg-attgcattttcagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTTAGT--------------------------------------------------------------------------
|| | | ||| |||| | | |||| | || || || | | | || | | | |||| | |||| | | ||| ||||| || ||||| ||||| |||||||||||||| | ||||| || |||| ||||||| ||||||||||||||||| ||| ||||||| ||
gtgagtctcttgattctaatcctctttagttaggaatatcttt-tgctgtactgagcttctgctactgctttgcttttcccaccgccacctgtcaa--tgctgacctagcactcttttagtttctcctttatatcaggactctctggaactagcttgttcaactcaattagtctgatggcctataatgttttctatacaagTCTTCCTGTGACGACTATAATTTTTGACAAGGATATCTCTGAGGAAACAGTACTGCAATATCCCCAGATTTTACTCTATTCTCAGTCTGGAAG
upper sequence: GLYMA12G33340.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os11g25980.2 (Oryza sativa), 3'ss of exon 21
--------------------attgttaatgattatgaatgttct-aatgc--tag-atgggcatccaatttctttata---------tagatctattctaaatttttcaaggtactgatgattgcattttcagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTTAGT
| || || |||| ||||| ||||| ||| || || | |||| | | || | ||| ||| || || |||| || || || || | ||||||||| ||| |||| ||| | ||||||| || || ||||| || ||||| |||||||||||||| || ||||| || || ||||||||||| || |
gtaagtcaaacttagtctggcatctttttgcttatttgagttcttaatgcaatagtattctcagtccatttatctgtaaaagaatgctggatatatgcttctcttatcaatgttctcatt-ttatgcatgcagTTTTTCTTTTCTTTCTGGTATTGCTGGAACAAGTCTATTCAACTCGGTTAGTTTGATGGCTTATAACGTCTTCTACACAAGCATTCCTGTTCTAACTACT
upper sequence: GLYMA12G33340.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G479163_T01 (Zea mays), 3'ss of exon 3
attgttaatgattatgaatgttctaatgctagatgggcatccaatttctttatatagatctattctaaatttttcaaggtactgatgat-tgcattttcagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTTAGT
|| || || | || || | || ||||| | | | ||| ||| | | | || || | || | ||||||||| ||| ||||||| | ||||||| ||| | ||||| || ||||| ||||||||||||||||||||||| || || |||||||| || || |
------gtaagccataaaccgtccgtacttgtat---tatggtagttggacgtatag-tgtgtgctagttttcttgat-tgctcatattctgtgcatgcagTTTTTCTTTTCTTTCAGGCATTGCTGGAACAAGCTTATTCAACTCAGTTAGTTTGATGGCTTATAATGTTTTCTACACAAGCATTCCTGTTTTAACTACT
upper sequence: GLYMA12G33340.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G037335_T01 (Zea mays), 3'ss of exon 7
---------------attgttaatgattatgaatgt-tctaatgctagatgggcatccaatttctttatatag-atctattctaaatttttcaaggtactgatgattgcattttcagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTTAGT
| || | ||| || || | | || | | || | | || | | | || || | | | | | ||| | | ||| || ||| | ||| | || || | ||||| |||||| | ||||| || ||||||||||||||||||| ||||||||||| ||| | || || | ||
gtgagttttccttgtaatgcttatgccattggctgcatttttcattacaagcttatgctactttgcactttggcatgggttttgtgggtgcaactgctcacttgagtccccttttagGTTTGCCTTTTTGTCGGGGCTATCTGGGACTAGCTTATTCAACTCAATTAGCTTGATGGCTTATAACGTTTTCTATACAAGTTTACCCGTCATGACTATA
upper sequence: GLYMA12G33340.1 (Glycine max), 3'ss of exon 21
lower sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 20
attgttaatgattatgaatgttctaatgctagatgggcatccaatttctttatatagatctattctaaatttttca--aggtactgatgattgcattttc--agTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTTAGT
| | | || | || |||| | || | |||| | | || | |||| | |||||| | | || | || || || ||||||||||| || |||||||| || || |||||||| |||||| ||||||||||||| |||||||| || |||||||||||||| ||||||
-------------gtaagt-ttattatctcagatatgttctcagt----------agatatcattcaagtcgttcatgaaatactgacaacagaatctatgtagCTTCTCGTTTATTTCAGGCGTTTCTGGAACCAGTCTTTTCAATTCAGTTAGCCTGATGGCTTATAACGTTTTCTACACCAGTGTTCCTGTTCTTGTTAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctttatatagatctattctaaatttttcaaggtactgatgattgcattttcagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTTAGT
tactgat putative branch site (score: 2)
cattttc putative PPT
tatatagatctattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgttaatgattatgaatgttctaatgctagatgggcatccaatttctttatatagatctattctaaatttttcaaggtactgatgattgcattttcagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTTAGT
- - - - - - - tgaatgt
- - - - - - - - - - - ctaatgc
- - - - - - - - - - - - - - - - - - gcatcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgatg