Sequence
atgc intronic sequence ATGC exonic sequence...ttttttggctgggattattttgtagttgttgttttaggtttgaccctttctccatctatataaaaatttaattagtttgtatcctcttgttgcattttagCCAGGAGAAAGCTTGGAGGAAGCTGTAAGAAGAGAAACATGGGAAGAGACTGGTATTGAAGTGGGAGAAGTTGTTTACCACAGTTCTCAGCCATGGCCTG
Basic information
| species | Glycine max |
| transcript | GLYMA17G12550.1 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G12550.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g04910.1 (Oryza sativa), 3'ss of exon 3
ttttttggctgggattatttt--gtagttgttgttttaggtt-tgaccctttctccatctat--ataaaaatttaattagtttgtatcctcttgttgcattttagCCAGGAGAAAGCTTGGAGGAAGCTGTAAGAAGAGAAACATGGGAAGAGACTGGTATTGAAGTGGGAGAAGTTGTTTACCACAGTTCTCAGCCATGGCCTG
| | || | | | | ||| | | || | | | | | | | || | | | | || ||| | || | | | || || |||||||||||||||||||| || || || ||||| ||||| |||||||||||||||||| |||| || ||||| |||| ||||||||||| || |||||||
--tgctaacttcaactttctgtggtactagcaagttcatttcattatcatcttgccgtgcactgaaagaagcttacacatgctgcaactgttcttt---ttgtagCCAGGAGAAAGCTTGGAAGAGGCAGTGAGAAGGGAAACGTGGGAAGAGACTGGTATTCAAGTTGGGGAAGTCATTTATCACAGTTCTCAACCGTGGCCTG
upper sequence: GLYMA17G12550.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G404897_T04 (Zea mays), 3'ss of exon 5
ttttttggctgggattattttgtagttgttgttttaggtttgacc-ctttctccatctatataaaaatt-taattagtttgtatcctct-----tgttgcattt-tagCCAGGAGAAAGCTTGGAGGAAGCTGTAAGAAGAGAAACATGGGAAGAGACTGGTATTGAAGTGGGAGAAGTTGTTTACCACAGTTCTCAGCCATGGCCTG
|| | || | | |||| | | |||| |||| || |||||| || | | || || ||| | | |||| ||| ||||||||||||||| |||| || || || ||| ||||||||||||| || |||||||| ||||| || |||| ||||| ||||||||||| ||||||||||
--------ctagcatgttgtctgtattgtagctaacaagatgactgtcttctttataagtataaacatcattacaagcttatatacattacatctgttatgtttgtagCCAGGAGAAAGCCTGGAAGAGGCAGTGAGACGAGAAACATGGGAGGAAACTGGTATCGAAGTTGGGCAAGTCGTTTATCACAGTTCTCAACCATGGCCTG
upper sequence: GLYMA17G12550.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G20070.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------------ttttttggctgggattattttgtagttgttgttt---tagg---tttgaccctttctccatctatataaaaatttaattagtttgtatcctct-tgttgcattt--tagCCAGGAGAAAGCTTGGAGGAAGCTGTAAGAAGAGAAACATGGGAAGAGACTGGTATTGAAGTGGGAGAAGTTGTTTACCACAGTTCTCAGCCATGGCCTG
||| | || ||| ||| | | | |||| || || || | | | || | |||| || ||||| ||| || ||| ||| |||||||| |||||||| || || ||||| || | ||||||||||||||||| || |||||||| ||||| ||||| |||||||| |||||||| |||||||
gtatgaaaacctcactgcgaaatcatctcaactcgatatttaataataactttctctttgtcattttttcatccaactcccctggataggccattccacttattttactcttgcatggagattt-----gtatgtataatctatgctgcttttgctagCCAGGGGAAAGCTTAGAAGAGGCTGTGAGGCGGGAAACATGGGAAGAGACAGGCATTGAAGTAGGAGATGTTGTATACCACAGCTCTCAGCCTTGGCCTG
upper sequence: GLYMA17G12550.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0016g04950.t01 (Vitis vinifera), 3'ss of exon 3
ttttttggctgggattattttgtagttgttgttttaggtttgaccctttctccatctat--ataaaaattta-attagtttgtatcctcttgttgcattttagCCAGGAGAAAGCTTGGAGGAAGCTGTAAGAAGAGAAACATGGGAAGAGACTGGTATTGAAGTGGGAGAAGTTGTTTACCACAGTTCTCAGCCATGGCCTG
| |||| || || |||||| || || | | | ||| || | | | | ||||| ||||||||| || | || |||| |||||||||||||||||||| ||||| || || |||||||||||||| ||||||||| ||||||||||||||||| | |||||||||||||||||||||||||
atatttgact--tatacttttgtcattttttgtcagctgacaaagttatcttaattttttaacgagaattttcattagtttgagtctttttattgc-ccctagCCAGGAGAAAGCTTGGAAGAAGCAGTGAGGAGAGAAACATGGGAGGAGACTGGTGTTGAAGTGGGAGAAGTTATCTACCACAGTTCTCAGCCATGGCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttctccatctatataaaaatttaattagtttgtatcctcttgttgcattttagCCAGGAGAAAGCTTGGAGGAAGCTGTAAGAAGAGAAACATGGGAAGAGACTGGTATTGAAGTGGGAGAAGTTGTTTACCACAGTTCTCAGCCATGGCCTG
atttaat putative branch site (score: 4)
tcctcttgtt putative PPT
atctatataaaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttttggctgggattattttgtagttgttgttttaggtttgaccctttctccatctatataaaaatttaattagtttgtatcctcttgttgcattttagCCAGGAGAAAGCTTGGAGGAAGCTGTAAGAAGAGAAACATGGGAAGAGACTGGTATTGAAGTGGGAGAAGTTGTTTACCACAGTTCTCAGCCATGGCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - ggctggg
- - - - - - - - - - - - gttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcttg
