Sequence
atgc intronic sequence ATGC exonic sequence...atcatattgttaaagaaatatggtctagcaaagctagatcttagtttatggttttaatttaattttggagagatggttgtgaatgatttgggtttggcagAGATATGCAGGATTGGGTACGAGGAGCAGAATGAGTGGTATTTCTTTAGCCACAAAGATAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
Basic information
species | Glycine max |
transcript | GLYMA02G05620.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G05620.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g38834.1 (Oryza sativa), 3'ss of exon 2
------atcatattgttaaagaaata--tggtctagcaaagctagatcttagtttatggttttaatttaattttgg--agagatggttgtgaatgatttgggtttggc----agAGATATGCAGGATTGGGTACGAGGAGCAGAATGAGTGGTATTTCTTTAGCCACAAAGATAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
| || || || | | ||| | | | | | | || | || | || | || | | | || | || ||| ||||| | || |||| |||||||| |||||||||||||||| |||||||| ||||| ||| |||| || | ||| || || || ||||| || || ||||| || || ||
gtttaattaatcttcatacatatatacttaatttcatgcatgcatagctagatcaatcgagctagctatatatagatcgatgctgatcatgcatggattggggtgggtgagaagAGCATTGCAGGATAGGGTACGAGGAGCAGAGCGAGTGGTACTTCTTCAGCTACAAGGACAGGAAGTACCCGACGGGGACGAGGACGAACAGGGCGACGAT
upper sequence: GLYMA02G05620.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G18060.1 (Arabidopsis thaliana), 3'ss of exon 1
atcatattgttaaagaaatatggtctagcaaagctagatcttagtttatggttttaatttaattttggagagatggttgtgaatgatttgggtttggcagAGATATGCAGGATTGGGTACGAGGAGCAGAATGAGTGGTATTTCTTTAGCCACAAAGATAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
|| | | || | || | | | | || ||| | ||||||| || ||| || | ||| ||| | | |||| ||| | || || || ||||| || ||||| |||||||| ||||| ||||| || |||||||||||||| ||||||||||| || ||||| |||||
-----gttacttaccgaacaccgt---gagatattttactttggtt-aaggtttta--ttgatt--------atcaccttaaat--tttaaatgttacagAACAATGTCGAATCGGTTATGAGGAACAAAATGAATGGTATTTTTTTAGTCACAAGGACAAGAAATATCCAACGGGGACAAGAACTAATAGAGCGACCAT
upper sequence: GLYMA02G05620.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G66300.1 (Arabidopsis thaliana), 3'ss of exon 1
atcatattgttaaagaaatatggtctag-caaagctagatcttagtttatggttttaatttaattttggagagatggttgtgaatgatttgggtttg------gcagAGATATGCAGGATTGGGTACGAGGAGCAGAATGAGTGGTATTTCTTTAGCCACAAAGATAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
|| | ||| |||| | || | | | | | | || | || | | || | || | | | | | || | ||||| ||| ||||| |||||||||||||| | |||||||||||||| ||||| | ||| ||||| ||||| |||||||| || || ||| |||||||| |
-------aatttatgaattatgatttaaacgataccacctacacatgtaagcaactatactgtgtagctcgaaagagtaatatgtaacctaaatgtgatacgtgtagAGAGATGTAGGATAGGGTACGAGGAGCAAACGGAGTGGTATTTCTTCAGCCATAGAGACAAGAAGTATCCGACTGGGACTAGGACAAACCGAGCCACCGT
upper sequence: GLYMA02G05620.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G36160.1 (Arabidopsis thaliana), 3'ss of exon 2
atcatattgttaaagaaatatggtctagcaaagctagatcttagtttatggttttaatttaat--tttggagagatggttgtga-----atgatttgggtttg--gcagAGATATGCAGGATTGGGTACGAGGAGCAGAATGAGTGGTATTTCTTTAGCCACAAAGATAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
| | ||| | || | || || ||| || || | | ||||| | | | || | | || | | ||| || | || || | ||||| ||| | || || || ||||| ||||| ||||||||||| |||||||||||||||||||||||||| || |||||||| |||||||| |||||
--gttttcacaaaatacatgatgcatacttaatttaggatttttttcttcttcttaatctgacaatgtgaatacatagatctgatgagcattaattatgtatattatagAGAGCTGCCGAATCGGATATGAGGAAAGAAATGAATGGTATTTCTTCAGCCACAAAGATAAGAAATATCCAACAGGAACAAGAACAAACAGAGCGACCAT
upper sequence: GLYMA02G05620.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 1
atcatattgttaaagaaatatggtctagcaaagctag-atcttagtttatggttttaatttaattttggagagatggttgtgaatgatttgggtttggcagAGATATGCAGGATTGGGTACGAGGAGCAGAATGAGTGGTATTTCTTTAGCCACAAAGATAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
| | || | || | | ||| || | | | | | || || | || || ||| ||| || | | |||||| |||| |||| ||||| || ||||||||||||||||||||||| |||||||| ||||||||||||||||| ||||| || ||||| ||||| |||||
ggctaacactttcataagctagccatcgcatttctgataagtaaatccgttgtgttttccttgttcaaagcgaataattg-atctgaattataatggacagAGAGATGCCGGATCGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT
upper sequence: GLYMA02G05620.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
-----atcat-attgttaaagaaatatggtctagcaaagctagatctt--------agtttatggttttaatttaattttggagagatggttgtgaatgatttgggtttggcagAGATA------TGCAGGATTGGGTACGAGGAGCAGAATGAGTGGTATTTCTTTAGCCACAAAGATAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
| | || | ||| | | ||| | | | | ||| | || || | | | | | | | |||| ||| ||||| || | | | ||| | ||||| | || ||||||| | |||||||| ||||| ||||||||||| |||||||| || || ||||| || |||||||||||||||
gtaagacggtcatccctcaagcttctcatttcggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: GLYMA02G05620.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
-----------atcatattgttaaagaaatatggtctagcaaagctagatctt----agtttatggttttaatttaattttggagagatggttgtgaatgatttgggtttggcagAGATA------TGCAGGATTGGGTACGAGGAGCAGAATGAGTGGTATTTCTTTAGCCACAAAGATAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
||| | | || | ||| | |||| ||| | || || | | | | | | | |||| ||| ||||| || | | | ||| | ||||| | || ||||||| | |||||||| ||||| ||||||||||| |||||||| || || ||||| || |||||||||||||||
gtaagacggtcatccctcaagcttctcatttcgggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatggttttaatttaattttggagagatggttgtgaatgatttgggtttggcagAGATATGCAGGATTGGGTACGAGGAGCAGAATGAGTGGTATTTCTTTAGCCACAAAGATAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
ttttaatttaattttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcatattgttaaagaaatatggtctagcaaagctagatcttagtttatggttttaatttaattttggagagatggttgtgaatgatttgggtttggcagAGATATGCAGGATTGGGTACGAGGAGCAGAATGAGTGGTATTTCTTTAGCCACAAAGATAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - -aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggagag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg