Sequence
atgc intronic sequence ATGC exonic sequence...agacatttatgagagaccttaaacatatttaaacttttttcctatgcgaaaaagtgcaattatatagaaattaaatcaattttgtggggtatttatagagCTTGATATGATGAGGGAAAGATTTGCAAAGCTTCTACTGGGGGAAGACATGTCTGGTGGTGGGAAAGGTGTCTGCACTGCAGTTACAGTATCAAATTCAA
Basic information
species | Glycine max |
transcript | GLYMA03G01560.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G01560.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G00460.1 (Arabidopsis thaliana), 3'ss of exon 2
agacatttatgagagaccttaaacatatttaaacttttttcctatgcgaaaaagtgcaattatatagaaattaaatcaattttgtggggtatttatagagCTTGATATGATGAGGGAAAGATTTGCAAAGCTTCTACTGGGGGAAGACATGTCTGGTGGTGGGAAAGGTGTCTGCACTGCAGTTACAGTATCAAATTCAA
|| || | | | ||| | || || | | | | | |||| | || | |||| | | ||| ||||| | |||| ||||||||| || ||||||||||| || ||||| ||||| || |||| ||||| || ||||||||||| || | ||||| |
-------------gtactgtagttttctctctttctttcttctctgttttcttctactgctttttttaaatgtctcatgtgttctagggtttgtgcagAACTTGAGACAATGAAGGAAAGATTCGCTAAGCTTCTACTTGGAGAAGATATGTCAGGGAGTGGTAAAGGAGTTTGCACTGCAGTGACTATCTCAAACGC--
upper sequence: GLYMA03G01560.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G45890.1 (Arabidopsis thaliana), 3'ss of exon 1
agacatttatgagagaccttaaacatatttaaacttttttcctatgcgaaaaagtgcaattatatagaaattaaatcaattttgtggggtatttatagagCTTGATATGATGAGGGAAAGATTTGCAAAGCTTCTACTGGGGGAAGACATGTCTGGTGGTGGGAAAGGTGTCTGCACTGCAGTTACAGTATCAAATTCAA
| || |||| ||| |||||| ||| | || | || | | ||||||| || | | |||||| || |||||||||||||||||||| ||||| | || || ||||||||||| || |||||||||| || || ||||| ||||| || ||||| ||
---------gtaaagtgtttaag---attgtaactttcttcttttg-------------tcatttcg---ttaaatcggggtttctag-----tgcagAGCTAGAGATGATGAGGGAAAGATTTGCGAAGCTGTTGCTTGGTGAAGACATGTCAGGAAGTGGGAAAGGAGTTTGTACTGCTGTTACTGTGTCAAACTC--
upper sequence: GLYMA03G01560.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0046g02530.t01 (Vitis vinifera), 3'ss of exon 1
agacatttatgagagaccttaaacatatttaaacttttttcctatgcgaa--aaagtgca-attatatagaaattaaatcaattttgtggggtattt---atagagCTTGATATGATGAGGGAAAGATTTGCAAAGCTTCTACTGGGGGAAGACATGTCTGGTGGTGGGAAAGGTGTCTGCACTGCAGTTACAGTATCAAATTCAA
| |||| | || | | | || || ||| || |||| | | || | | | | || ||||||||| |||||| |||||||||| | |||||| | ||||| ||||||||||| || | || ||||| ||||||||||| || ||| | |||||| |
----------------------gtgggtccaaacctcatttccggggaagctaaggtctggattctaatctgcttaactaacttgtatttgattttctgggcagAGCTTGAACTGATGAAGGAAAGATTTTCCAAGCTTTTGCTGGGTGAAGACATGTCAGGAAGCGGCAAAGGCGTCTGCACTGCGGTCACAATCTCAAATGC--
upper sequence: GLYMA03G01560.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S28_109V6.1 (Physcomitrella patens), 3'ss of exon 2
agacatttatgagagaccttaaacatatttaaacttttttcctatgcgaaaaagtgcaattatatagaa--attaaatc-aattttgtggggtatttatagagCTTGATATGATGAGGGAAAGATTTGCAAAGCTTCTACTGGGGGAAGACATGTCTGGTGGTGGGAAAGGTGTCTGCACTGCAGTTACAGTATCAAATTCAA
| | || | | | || || ||| || | | | | || || | ||| || ||| | | | || ||| | || ||||||| ||| | |||||||||||||| || ||||| || ||||||||||| || |||||||| |||||||| | | |||| || ||
ggtctgctaccaagcgagcttcctaccgttgcacatttgacc-agccattttatttcagttgcgagtgattgttatttctgattactttttgcttctacagAAGTGGAGATGATGAAGGAGAAGTTTGCAAAGCTTCTGCTTGGGGAGGATATGTCTGGTGGGGGAAAAGGTGTTTGCACTGCGTTGGCTATATCGAACTC-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcgaaaaagtgcaattatatagaaattaaatcaattttgtggggtatttatagagCTTGATATGATGAGGGAAAGATTTGCAAAGCTTCTACTGGGGGAAGACATGTCTGGTGGTGGGAAAGGTGTCTGCACTGCAGTTACAGTATCAAATTCAA
aattatatagaaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agacatttatgagagaccttaaacatatttaaacttttttcctatgcgaaaaagtgcaattatatagaaattaaatcaattttgtggggtatttatagagCTTGATATGATGAGGGAAAGATTTGCAAAGCTTCTACTGGGGGAAGACATGTCTGGTGGTGGGAAAGGTGTCTGCACTGCAGTTACAGTATCAAATTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - cctatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - agtgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtggg