Sequence
atgc intronic sequence ATGC exonic sequence...taaaataataatccaccccttagttttaattatcaccacttatttattttttcatgcatgttgactggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT
Basic information
species | Glycine max |
transcript | GLYMA07G03890.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
taaaataataatccaccccttagttttaatta---tcaccacttatttatt----ttttcatgcatgttgactggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT
|| | | | | || ||||| ||| || | || | || | || ||||| | | | || | | || | | | |||| ||||||||||||||||||||||| ||||||||||| ||||||||||| || || || || ||||||| || |||||||||||||||||||| || |
---gattctgttgttgtagtaaaattaaattaatctcaaatctagtatagtgtaattatagtgtatgttagtaattatagtaattatagtgtattc----atttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 11
------taaaataataatccaccccttagttttaattatcacca-cttatttattttttcatgcatgttgactggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT
| |||| || | | ||| | || | | | | ||| | || || | | ||||| | || | | | | | || | | | ||||||||||||||||||| ||||| || ||||||||||| ||||||||||| || || || || ||||| | ||||||||||||||||||||||| || |
cggttttgaaattgtacttgtcgggttaaat--aaatgtgatgaacttttctacgttctggtttatgtttgcatgttattaa-taatagtgtattc----atttcagAGTTTAAGGCACAATCCAAATGGAAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACCGCATTGGCATGGAGAAATAGATCATTCGGGT
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 11
-taaaataataatccaccccttagttttaattatcaccacttatttatttt-ttcatgcatgttgactggtgtctgacttg-tgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT
| | | | | ||| ||| | || || ||| || || ||| ||| | ||| ||| | || | | | || | | |||||||||||||||||||||||||||| ||||| ||||| ||||||||||| || || || |||||||| | || ||||||||||| ||||||||||| |
atcatgattttttttaaaacttgttttgtgtcatgcataccagcatatcttatttgtgctagttta--ggttaatgatatactggtgtgatatt-tgtttcagAGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGAGAATACATAATATACACAGCCTTAGCATGGAGAAACAGATCATTTGGGT
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 11
--taaaataataatccaccccttagttttaatt-atcaccacttatttattttttcatgcatgttgactggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT
| ||| || || | | || || | || ||| | |||||| ||| ||| || | | | || | | | || | | |||| ||||| ||||||||||||||||| ||||||||||| ||||||||||| || || || |||||||| | || ||||||||||||||||||||||| |
gtttgaattatcatgattttttaaaacttgttttgtggtcatgtatatctttttt-gtgctggtttac-attattaatatactggtgtgatatt-tgtttcagAGCTTAAGACACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATATACACAGCATTAGCATGGAGAAATAGATCATTTGGGT
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 12
---------taaaataataatccaccccttagttttaattatcaccacttatttattttttcatgcatgttgactggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT
|| || || |||| || |||||| | | || | |||| | || | | || || | | | | | || | |||||||| |||||||||| |||||||||||||||| ||| ||||||||||| ||||| ||||| ||||| | | ||||||||||||||||| ||||| |
tttttttatggaaggaaaaaggcaccggtt--ttttaaaagttagttctaacttatgctaggatatttaaaaaacagtaactaatcctt--tctgttctt-----ccagAGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGAGAGTACATTATCTACACAGCGCTAGCATGGAGAAATAGATCCTTTGGGT
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
-taaaataataatccacccct-tagttttaattatcaccacttat-ttattttttcatgcatgt-tgactggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT
| | |||||| | | | |||| | | |||||||| |||| | | | | ||| | | |||| || | |||| || | ||| || || ||||| |||| |||||||| ||||||||||| ||||| || || || |||| |||| ||||| |||||||||||||| |
ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatctgattgtgagtaatcattttggttggtc----agAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 11
--------taaaataataatccaccccttagttttaattatcaccacttatttattttttcatgcatgttgactggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT
||| | || | | || || | ||| | ||| | | || ||| |||| |||||| | |||| | ||| || | |||| || | |||||| || |||||||||||||| || || ||||| || || || ||||| || ||||| | |||||| ||||||||||| ||||||||||
aagtgcctcaaagttatgggt-atcgctaagccgcgtct-tcagaatatatatctgttctcac-----ttgatctgtgtctcatatgtgggt-actcttgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGAGAATATATAATCTACACGGCTTTGGCTTGGAGAAATAGGTCATTTGGTT
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 15
-taa-aataataatccaccccttagttttaattatcaccacttatttattttttcatgcatgttgactggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT
|| || || | | |||| |||| ||| || | | | || | | | ||| | || | | ||| | | |||| || | |||||| || ||||| |||||||| || |||||||||||||| ||||||||||| ||||||| ||||| ||| ||||||| |||||||| |
ttactggtattagtaagaaatatgaccttaa--atcatttattaattttgtgactacccactgtcatttatgtttctattatttaattttttgctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
-----taaaataataatccaccccttagttttaattatcaccacttatttattttttcatgcatgttgac-tggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT
| |||| ||| | | || |||| | ||| | | | | | || | || | | | || || || | | | || | | | |||| ||| || | |||||| || |||||||||||||| || || || || ||||| ||||| || || ||||||| |||||| |||||||||||||| ||||| |
taatagatgataaaaatgaaactct--gtttca--tatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatat-agctattctaactctca-gAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 11
taaaataataatccaccccttagttttaattatcaccacttatttatttttt--catgcatgttgac---tggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT
| ||| | | | | | | || ||||| | || |||| || || ||||| || | | | || | ||| |||| | | |||| ||| || || || |||||||||||||||||||||||||||||||| ||||| |||||||| || | |||||||||||| ||||| || |||||||
----gcattaagctagga-tgaatgattgtttccaccatattttaatttattgttatttatgtttacatttatttcttccttttttttttttttttgtgtttcagAGCCTAAAACATAACCCAAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGTGAGTACATTATATATACAGCTTTGGCATGGAGGAATAGGTCTTTTGGTT
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
taaaataataatccaccccttagttttaattatcaccacttattta-ttttttcatgcatgttgactggtgtctgacttgtgatttact--tttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT
| | | || | ||| | || | | | |||||| | |||| |||||| || ||| | ||| | | ||||||| | ||||||| | ||||| |||| ||||||||||||||| |||||||| || || |||||||| ||||||||||||||||||||||||||| |
---actttttctctaagaggcagtgcatagaatatgtgcgggctcagtttttttgttgtcacattatggttaatgacttttgtttttttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S243_63V6.1 (Physcomitrella patens), 3'ss of exon 11
----taaaataataatccaccccttagttttaattatcaccacttatttattttttcatgcatgttgactggtgtctga---cttgtgatttacttttatactca----agAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT
| | | || | | ||| || | ||| | | || | || || | || ||| ||| | || ||| | | |||| | | || ||||||||||| |||||||| || |||||||| ||||| ||||||||||| ||||| | | | || ||||| ||| ||||||||||||
gtgaccgattgctcgtctaaatttctttttgaaatttcatcttcgaaagatatgtttgctcaaaatatctatcaagtgaacgcttatcggttggctttgtgtgccttgcagAGCCTGAAACATAATCCGAATGGCAGGTTTGTGGTAGTTTGTGGTGATGGTGAGTATATTATCTACACAGCTCTTGCTTGGAGGAATCGATCATTTGGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttttcatgcatgttgactggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT
gtctgac putative branch site (score: 3)
tttactttt putative PPT
tgatttacttttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaaataataatccaccccttagttttaattatcaccacttatttattttttcatgcatgttgactggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
-aaaataa
- - - - - - ccacccc
- - - - - - - - - - - - - - - - tcaccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acttgtg