Sequence
atgc intronic sequence ATGC exonic sequence...tgagtttctgtatgtttttctttcattttgtagaaaagggcatctgataaatttgattttttttttttgtgtgtgtgatttgggttcttaattgatgcagATATAGAGCATTCGATGAGTATCAAGGGATTGAAGTTGCTTGGAACCAGGTCAAGTTGTATGATTTCCTGCAAAGCCCTGAAGATCTTGAGAGGCTTTAC
Basic information
species | Glycine max |
transcript | GLYMA10G30210.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G30210.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G28080.2 (Arabidopsis thaliana), 3'ss of exon 2
tgagtttctgtatgtttttctttcattttgtagaaaagggcatctgataaatttgattttttttttttgtgtgtgtgatttgggttcttaattga----tgcagATATAGAGCATTCGATGAGTATCAAGGGATTGAAGTTGCTTGGAACCAGGTCAAGTTGTATGATTTCCTGCAAAGCCCTGAAGATCTTGAGAGGCTTTAC
|| | | || ||||| | |||| || | | | | | | | | | ||| ||||| | | ||||| ||||| || |||| ||| |||||||||||||| || ||||| || |||||||| || ||| | || |||||| |||| || ||| |||| || |||||||| |||
cgaaaaaggttgaaatctttgatcattaaacaaaaaatgg-gtttagtgattctaaactagaaaaagactatgtt---tttggttccataatttggatttgcagTTACAGAGGATTTGATGAGTATCAAGGTATAGAAGTAGCATGGAACCAAGTAAAGCTCTACGATTTCTTGCAGAGTCCTCAAGAGCTAGAGAGGCTCTAC
upper sequence: GLYMA10G30210.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G04910.1 (Arabidopsis thaliana), 3'ss of exon 2
tgagtttctgtatgtttttctttcattttgtagaaaagggcatctgataaatttgattttttttttttgtgtgtgt-gatttgggttcttaatt--gat---gcagATATAGAGCATTCGATGAGTATCAAGGGATTGAAGTTGCTTGGAACCAGGTCAAGTTGTATGATTTCCTGCAAAGCCCTGAAGATCTTGAGAGGCTTTAC
||| ||| ||| | || | | | | | ||| || ||| | | | | || | ||||| || ||| | || ||||||||||| ||||| ||| |||| || ||||| || |||||||| || ||| | ||||||||||| ||||||||||| ||||||||||||||||||
------tctttattgctttgacttataccaaattcagattctgcaaacaaaaaaacttctttgctcatacatacattaatcttctttctttcttttgattttgtagTTATAGAGCATTTGATGAATATGAAGGCATAGAAGTAGCATGGAACCAAGTTAAGCTATATGATTTCCTACAAAGCCCTGAGGATCTTGAGAGGCTTTAC
upper sequence: GLYMA10G30210.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0020g03380.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------tgagtttctgtatgtttttctttc-----attttgtag--------aaaagggcatctgataaatttgattttttttttttgtgtgtgtgatttgggttcttaattgatgcagATATAGAGCATTCGATGAGTATCAAGGGATTGAAGTTGCTTGGAACCAGGTCAAGTTGTATGATTTCCTGCAAAGCCCTGAAGATCTTGAGAGGCTTTAC
| ||| || | | ||| | ||| ||| | || ||| || || | | ||| |||| | | | || | | ||| |||||||| ||||| |||||||||||| ||||||||||||| || ||||||||||| ||| | ||||||||||||| || |||||||| || |||||||| |||
gtatgagacttttctgcataaccttctcaaatttttgaagaatcctctcttttggaattctgtggctttttttgaatgggtattctctagctctccatttaaagggttgtctttttttcttcctgtaatgatttttgcagATACAGAGCCTTCGATGAGTATGAAGGGATTGAAGTAGCCTGGAACCAGGTGAAGCTTAATGATTTCCTGCAGAGTCCTGAAGAGCTGGAGAGGCTGTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gataaatttgattttttttttttgtgtgtgtgatttgggttcttaattgatgcagATATAGAGCATTCGATGAGTATCAAGGGATTGAAGTTGCTTGGAACCAGGTCAAGTTGTATGATTTCCTGCAAAGCCCTGAAGATCTTGAGAGGCTTTAC
atttgatttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgagtttctgtatgtttttctttcattttgtagaaaagggcatctgataaatttgattttttttttttgtgtgtgtgatttgggttcttaattgatgcagATATAGAGCATTCGATGAGTATCAAGGGATTGAAGTTGCTTGGAACCAGGTCAAGTTGTATGATTTCCTGCAAAGCCCTGAAGATCTTGAGAGGCTTTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- -gtttctg
- - - - - - - - - - - - - - - - - - - -gcatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtgtg