Sequence
atgc intronic sequence ATGC exonic sequencegtttttaatttgtgcttaaaacatcactctatttcattcttcaagataacttttttcccttttaccctgaactcagatttatttgtgattttttgttcagTATGCTGAAGATCTTGAAAGTGGTTTCATGTCAGATGTGGAATCTAAATACAAGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAA
Basic information
species | Glycine max |
transcript | GLYMA09G31920.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G31920.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os03g50300.1 (Oryza sativa), 3'ss of exon 14
gtttttaatttgtgcttaaaacatcactctatttcattcttcaagataacttttttcccttttaccctgaactcagatttatttgtgattttttgttcagTATGCTGAAGATCTTGAAAGTGGTTTCATGTCAGATGTGGAATCTAAATACAAGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAA--
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-------------gtttata----cacatcctttcaaggg--aaaatagcaaaatccacagcattctagcttttgacctttgttacattgtgttttgcagTATGCAGAAGATGTTGAAAGTGGTTCT---TCAGATGTTGAGACGAAGTACAAGAAAATGTATGAGGATGACATAAATCCTTTTGCTGCTTTTTCAAAGAAG
upper sequence: GLYMA09G31920.1 (Glycine max), 3'ss of exon 17
lower sequence: AT3G18480.1 (Arabidopsis thaliana), 3'ss of exon 15
gtttttaatttgtgcttaaaacatcactctatttcattcttcaagataacttttttcccttttaccctgaactcagatttatttgtgattttttgttcagTATGCTGAAGATCTTGAAAGTGGTTTCATGTCAGATGTGGAATCTAAATACAAGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAA
|| ||| ||| ||| | |||| | || | | ||| | | | | |||| || | | || ||| || | ||||||| ||||||||||||||||| |||| || ||||| ||||| ||||||||||| || || || ||||| || || |||||||| |||||||| ||||
gtatttgttttctgc--gatacatttccct---tgaaccttttctgtctcgtgatcgggttttttccatggttgatatcgttttccaatct------cagTATGTGGAAGATCTTGAAAGTGGATTCAGCTCGGATGTCGAATCAAAATACAAGAAAATTTACGAAGATGACATCAACCCTTTTGCAGCATTCTCGAAAA
upper sequence: GLYMA09G31920.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv17s0000g03970.t01 (Vitis vinifera), 3'ss of exon 15
gtttttaatttgtg-cttaaaacatcactctatttcattcttcaagataacttttttcccttttaccctgaactcagatttatttgtgattttttgttcagTATGCTGAAGATCTTGAAAGTGGTTTCATGTCAGATGTGGAATCTAAATACAAGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAA
|| |||| || || | || | | | | | ||| | |||| | | || | || ||| | ||||||| || | ||||||||||| |||||||||| |||||||| ||||| || |||||||||||||||||||||||||||||||| |||||||| ||||| ||||
-----------gtatcttatcgcaattctatgcttattaaattatggttgtcatttcctcttt---cttaaatttcatcttctttaa----tcatgttcagCATTCAGAAGATCTTGAGAGTGGTTTCAGCTCAGATGTTGAATCCAAGTACAAGAAGATATATGAGGATGATATAAATCCCTTTGCTGCTTTCTCCAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataacttttttcccttttaccctgaactcagatttatttgtgattttttgttcagTATGCTGAAGATCTTGAAAGTGGTTTCATGTCAGATGTGGAATCTAAATACAAGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAA
agataac putative branch site (score: 3)
ttttttgttc putative PPT
atttatttgtgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttaatttgtgcttaaaacatcactctatttcattcttcaagataacttttttcccttttaccctgaactcagatttatttgtgattttttgttcagTATGCTGAAGATCTTGAAAGTGGTTTCATGTCAGATGTGGAATCTAAATACAAGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC