Sequence
atgc intronic sequence ATGC exonic sequencegtatatacttttaaatttcacatgaactatgattattgattcatgtcattctagctgcggaagtgacaagatatgcttatctttgtcaatgcaactctaaaattaagtagctagcaaggagctaaaactaatcatttgtacgtatatttcagGTGATGACACAGGCAGATTTAGGCCTTGCAGATGCATATATCAATGGGGACTTTTCATTTGTTGATAAAGATGAAGGTCTCTTGAATCTTATTTTG
Basic information
species | Glycine max |
transcript | GLYMA20G34340.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G34340.1 (Glycine max), 3'ss of exon 14
lower sequence: AT3G23460.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatatacttttaaatttcacatgaactatgattattgattcatgtcattctagctgcggaagtgacaagatatgcttatctttgtcaatgcaa-ctctaaaattaagtagctagcaaggagctaaaact-aatcatttgtacgtatatttcagGTGATGACACAGGCAGATTTAGGCCTTGCAGATGCATATATCAATGGGGACTTTTCATTTGTTGATAAAGATGAAGGTCTCTTGAATCTTATTTTG
| | | || | ||| | | ||| ||| | | ||||| || | | ||| || || || | || | |||| |||| || | || || || | ||| ||||| |||||||||| |||||||| ||||| ||||| ||||||||||| || ||||||||||| |||| || ||| || |||||||| || ||
---------------------gttagcctagaacaccgat--gttagaacttagg-atagaacttaaaagat-cactc-tttgaatcagtggaaactgtttttttctgaagct--caagaagtggattcttgatgatgctt---tatcacacagGTTATGACACAGGTTGATTTAGGACTTGCTGATGCTTATATCAATGGAGATTTTTCATTTGTCAATAAGGAAACAGGACTTTTGAATCTGATCATG
upper sequence: GLYMA20G34340.1 (Glycine max), 3'ss of exon 14
lower sequence: AT3G23510.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatatacttttaaatttcacatgaactatgattattgattcatgtcattctagctgcggaagtgacaagatatgcttatctttgtcaatgcaactctaaaattaagtagctagcaaggagctaaaactaatcatttgtacgtatatttcagGTGATGACACAGGCAGATTTAGGCCTTGCAGATGCATATATCAATGGGGACTTTTCATTTGTTGATAAAGATGAAGGTCTCTTGAATCTTATTTTG
| | || | | | | | | || | | | || | || || ||| | | | ||||| | | || || | | | | | |||| |||||||| || |||||||| ||||||||||| ||||||||||| || ||||| || ||||||||||| ||| || || ||||| ||| ||
----------------------------------gtacaaatatataaatatgacaatgaaaattttgaatagtctttttattattccatg-atttttgaaatttgattcttg-----------------attcttgatttttgtctcttagGTTATGACACAAGCGGATTTAGGACTTGCAGATGCTTATATCAATGGAGATTTTTCTTTCGTTGATAAAGAATCAGGACTTTTAAATCTGATTATG
upper sequence: GLYMA20G34340.1 (Glycine max), 3'ss of exon 14
lower sequence: AT3G23480.2 (Arabidopsis thaliana), 3'ss of exon 3
gtatatacttttaaatttcacatgaactatgattattgattcatgtcattctagctgcggaagtgacaagatatgcttatctttgtcaatgcaactctaaaattaagtagctagcaaggagctaaaactaatcatttgtacgtatatttcagGTGATGACACAGGCAGATTTAGGCCTTGCAGATGCATATATCAATGGGGACTTTTCATTTGTTGATAAAGATGAAGGTCTCTTGAATCTTATTTTG
|| |||| | || | || |||||| | | ||| | || |||| | |||| | | | | | |||| ||||||| ||||||||||| ||||||||||| ||||||||||| || ||||| || || |||||||| ||| || |||||||| ||| ||
-----------------------------------------------------------------gtaacatatatacaaagacaaaaa-gaaaagttaaaatagactttctatagctcaaatagaact--tgattttt---tttctcttagGTTATGACACTAGCAGATTTAGGACTTGCAGATGCTTATATCAATGGAGATTTTTCTTTCGTCGATAAAGACTCAGGACTTTTGAATCTGATTATG
upper sequence: GLYMA20G34340.1 (Glycine max), 3'ss of exon 14
lower sequence: AT3G23530.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatatacttttaaatttcacatgaactatgattattgattcatgtcattctagctgcggaagtgacaagatatgcttatctttgtcaatgcaactctaaaattaagtagctagcaaggagctaaaactaatcatttgtacgtatatttcagGTGATGACACAGGCAGATTTAGGCCTTGCAGATGCATATATCAATGGGGACTTTTCATTTGTTGATAAAGATGAAGGTCTCTTGAATCTTATTTTG
| | | | ||||| || | | ||| |||| | | || || | || || | | | |||||||| |||||||| || |||||||| ||||||||||| ||||||||||| || ||||| || ||||||||||| ||| || || ||||| ||| ||
--------------------------------------------------------gtacatatatataaatatgacaatgaatagttggaatagtcttttattattccatgatctttgaact----ttgattcttgattcttgattttcagGTTATGACACAAGCGGATTTAGGACTTGCAGATGCTTATATCAATGGAGATTTTTCTTTCGTTGATAAAGAATCAGGACTTTTAAATCTGATTATG
upper sequence: GLYMA20G34340.1 (Glycine max), 3'ss of exon 14
lower sequence: AT3G23470.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatatacttttaaatttcacatgaactatgattattgattcatgtcattctagctgcggaagtgacaagatatgcttatctttgtcaatgcaactctaaaattaagtagctagcaaggagctaaaactaatcatttgtacgtatatttcagGTGATGACACAGGCAGATTTAGGCCTTGCAGATGCATATATCAATGGGGACTTTTCATTTGTTGATAAAGATGAAGGTCTCTTGAATCTTATTTTG
|| ||||| || | |||| | || || | ||| |||| | || || | | | | | |||| |||||||| ||||||||||| || |||||||| ||||||| ||| || ||||| || || |||||||| ||| || |||||| | ||| ||
-----------------------------------------------------------------gtaatttatgcataa----gacaataagag---aagtttgaaaagcctttctatagctc---ttgattcttgattctcttctcttagGTTATGACACAAGCAGATTTAGGACTCGCAGATGCTTATATCAGTGGAGATTTTTCTTTCGTCGATAAAGACTCAGGACTTTTGAATTTGATTATG
upper sequence: GLYMA20G34340.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv05s0049g01620.t01 (Vitis vinifera), 3'ss of exon 9
gtatatacttttaaatttcacatgaactatgattattgattcatgtcattctagctgcggaagtgacaagatatgcttatctttgtcaatgcaactctaaaattaagtagctagcaaggagctaaaactaatcatttgtacgtatatttcagGTGATGACACAGGCAGATTTAGGCCTTGCAGATGCATATATCAATGGGGACTTTTCATTTGTTGATAAAGATGAAGGTCTCTTGAATCTTATTTTG
| || || | | ||| | | | | | || | || || || || | ||||||| | | | ||| || ||| | ||||| || | |||||||| |||||||||||||||||||||||||||||||| || ||||| ||||||||||||| ||||| || | |||| | ||
------------------------------aagggtttttttttcttatttttttt------ttctcttggtacaatcatattgttctataga----caaaatta--tcacca-caattgaacaacacttgcattctgtac---------agATTGCTACACAGGCTGATTTAGGCCTTGCAGATGCATATATCAATGGAGATTTTTCTCTTGTTGATAAAGACGAAGGGCTTCAAAGTCTTTTCATG
upper sequence: GLYMA20G34340.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv05s0049g01650.t01 (Vitis vinifera), 3'ss of exon 13
gtatatacttttaaatttcacatgaactatgattattgattcatgtcattctagctgcggaagtgacaagatatgcttatctttgtcaatgcaactctaaaattaagtagctagcaagga-gctaaaactaatcatt-tgtacgtatatttcagGTGATGACACAGGCAGATTTAGGCCTTGCAGATGCATATATCAATGGGGACTTTTCATTTGTTGATAAAGATGAAGGTCTCTTGAATCTTATTTTG
| | || | ||| | | || || || ||| | | | | || | | || | | | || ||| | |||||||| |||||||||||||||||||||||||||||||| || ||||| ||||||||||||| ||||| ||
----------------------------------------------------------------------gtct-tttttttttcttggttgaatcatattgttctatagacaaaattatcaccacaattgaacagCACTTGCATTCTTTACAGATTGCTACACAGGCTGATTTAGGCCTTGCAGATGCATATATCAATGGAGATTTTTCTCTTGTTGATAAAGACGAAGGGCTTC-------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaaattaagtagctagcaaggagctaaaactaatcatttgtacgtatatttcagGTGATGACACAGGCAGATTTAGGCCTTGCAGATGCATATATCAATGGGGACTTTTCATTTGTTGATAAAGATGAAGGTCTCTTGAATCTTATTTTG
aactaat putative branch site (score: 2)
taaaactaatcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatacttttaaatttcacatgaactatgattattgattcatgtcattctagctgcggaagtgacaagatatgcttatctttgtcaatgcaactctaaaattaagtagctagcaaggagctaaaactaatcatttgtacgtatatttcagGTGATGACACAGGCAGATTTAGGCCTTGCAGATGCATATATCAATGGGGACTTTTCATTTGTTGATAAAGATGAAGGTCTCTTGAATCTTATTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG