Sequence
atgc intronic sequence ATGC exonic sequence...agaagtgagttttaaaataatagtccttattgcgggttcaattatcagcaatatttgttttatgggtggtggctgattgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
Basic information
species | Glycine max |
transcript | GLYMA15G01680.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 11
agaagtgagttttaaaataatagtccttattgcgggttcaattatcagcaatatttgttttatgggtggtggctg---attgttgatttcatt-tattg--tgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
||||| |||| || | | | | | | | | || ||| | || || || || || | | |||| | |||| ||||| ||||||||||||||| || ||||||||||||||||||||||| || ||||| || ||||| |||||||||||||||||||| ||||| || |
------cggttttgaaattgtacttgtcgggttaaataaatgtgatgaacttttctacgttctggtttatgtttgcatgttattaataatagtgtattcatttcagAGTTTAAGGCACAATCCAAATGGAAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACCGCATTGGCATGGAGAAATAGATCATTCGGGT
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
agaagtga-gttttaaaataatagtccttattgcgggttcaattatcagcaatatttgt-tttatgggtggtggctgattgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
|| ||| || | ||| | || | | | | | ||| | || | | | || | | | | | ||| ||| |||| |||| ||||||||| |||||||| ||||||||||||||||||||||| || ||||| || ||||||||||| |||||||||||||| ||||| || |
gattctgttgttgtagtaaaattaaattaatctcaaatctagtatagtgtaattatagtgtatgttagtaattatagtaattatagtgtattcattt--cagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 11
agaagtgagttttaaaataatagtccttattgc-gggt----tcaattatcagcaatattt---gttttatgggtggtggctgattgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
| | || || | ||| | | ||| | | || | | |||| | | ||| | || ||| || | || ||| |||| |||||||| || || ||||| || ||||| || || |||||||||||||| | ||| || || ||||||||||| ||||| |||||||||||||| |
-------ggctacaacatttcttttctttctactaggtaatgttagttgtttgtcatatcttgaatagtattcaatcttactatgtgtc-atctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 11
agaagtgagttttaaaataatagtccttattgcgggttcaattatcagcaatatttgttttatg--ggtg---gtggctgat-tgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
|| | ||| || || | ||| | ||| | ||| |||| | |||| || ||| | | || | || | | || | | | |||| |||| |||||||| |||||||| ||||||||||||||||||||||| || ||||| |||||||| ||||| |||||||||||||| |||||||| |
----gtttgaattatcatgat--tttttaaaacttgttttgtggtcatgtatatcttttttgtgctggtttacattattaatatactggtgtgatatttgtttcagAGCTTAAGACACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATATACACAGCATTAGCATGGAGAAATAGATCATTTGGGT
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 12
-----agaagtgagttttaaaataatagtcctt--attgcgggttcaattatcagcaatatttgttttatgggtggtggctgattgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
| | || || | || || | | |||| | | || | | ||| | || || || || | | || |||| |||| |||||||||||||||||||||||||| ||||||||||||||| ||||||||||| ||||| || | |||||||||||||| || ||||| |
tttttttatggaaggaaaaaggcaccggttttttaaaagttagttctaacttatgctaggat-atttaaaaaacagtaactaatcctttctgttcttc------cagAGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGAGAGTACATTATCTACACAGCGCTAGCATGGAGAAATAGATCCTTTGGGT
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 11
agaagtgagttttaaaataatagtccttattgcgggttcaattatcagcaatatttgttttatgggtggtggctgat-tgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
||| |||| | || || | | | | ||||||| || ||| |||| | || | | || | | | |||| ||||| ||||||||| |||||||| ||||| ||||||||||||||||| || ||||| |||||||| || || ||||||||||| || |||||||| |
-atcatgattttttttaaaacttgttttgtgtcatgcataccagcatatcttatttgtgctagtttaggttaatgatatactggtgtgatatttgtttcagAGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGAGAATACATAATATACACAGCCTTAGCATGGAGAAACAGATCATTTGGGT
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 10
---------------------------------------------------------agaagtg-agttttaaaataatagtccttattgcgggttcaattatcagcaatatttgttttatgggtggtgg---ctgattgt---tgatt-tcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
|||| ||||| || | || || | || | | | | | | |||| || | || |||||||| | ||| | || ||| |||| || ||||| ||||| ||||| |||| ||||||||||||||||||||||||||||| || || ||||| |||| ||||| |||||||||||||| |
gtacttttggatgctgatgtgttctttgtattttaaaacttgttactattgtaggtttatagtgtggtttttaagtggacatcttttc----gttttattatttggtggtgctcattttgtgtggcgtataatctgattgtgattaattatttttggttggtcagAGCTTGAAGCATAATCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGTGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGGTCATTTGGAT
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
agaagtgagttttaaaataatagtccttattgcgggttcaattatcagcaatatttgttttatgg----gtggtggctgattgt---tgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
|| | || | | | || | | | | |||| | || |||||||| | || || ||| |||| || ||||| || || ||||| |||| |||||||||||||||||||| |||||||| || || ||||| |||| ||||| ||||| |||||||| |
-------ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G15980.5 (Arabidopsis thaliana), 3'ss of exon 11
---------------agaagtgagttttaaaataatagtccttattgcgggttcaattatcagcaatatttgtttta--tgggtggtggctgattgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
|| || | ||||| | | || | | | | || | || | || || || | | | | | | | |||| || |||||||| || |||||||||||||| || || || || ||||| |||||||| || |||||||| ||||| ||||||
atttgaaatgaagcgttaatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagCTATTCTAACTCT-CAGAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGA----------------
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 11
agaagtgagttttaaaataatagtccttattgcgggttcaattatcagca---atatttgtttta---tgggtggtggctgattgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
||||| | ||| | || | | | | | |||| | |||| |||| | || ||| || || || | | || |||| || |||||||| || |||||||||||||| || || ||||| || || || || || || ||||| || ||||| ||||||||||||||||||||||
--aagtg--cctcaaagttatgggtatcgcta--agccgcgtcttcagaatatatatctgttctcacttgatctgtgtctcatatgtgggtactcttgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGAGAATATATAATCTACACGGCTTTGGCTTGGAGAAATAGGTCATTTGGTT
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 15
agaagtgagttttaaaataata-gtccttattgcgggttcaattatcagcaatatttgtt-ttatgggtggtggctgattgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
| | || || |||| | ||||| | | | | | | || | | || || | ||| || | || || || | |||| || |||||||| || ||||| |||||||| || || ||||||||||||||||| ||||| |||||||| ||||| ||| |||||||||||||||| |
ttactggtattagtaagaaatatgaccttaaatcatttattaattttgtgactacccactgtcatttatgtt--tctattatttaattttttgctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
agaagtgagttttaaaataatagtccttattgcgggttcaattatcagcaatatttgtttta--tgggtggtggctgattgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
|| || | ||||| | | || | | | | || | || | || || || | | | | | | | |||| || |||||||| || |||||||||||||| || || || || ||||| |||||||| || |||||||| ||||| ||||||||||| || ||||| |
-taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagctattctaactct-cagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 11
agaagtgagttttaa--aataatagtccttattgcgggttcaattatcagcaatatttgttttatgggtggtggctgattgttgatttcatttattgtg-cagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
| | | || | | ||| || || | || | |||| | || | ||||| | | | | || || ||| ||| ||| |||| |||| || || ||||||||||||||||||||||| |||||||||||||||||||||||||| || || ||||||||||| |||||||| |||||||
-gcattaagctaggatgaatgattgtttccaccatattttaatttatt-gttatttatgttt-acatttatttcttccttttttttttttttttgtgtttcagAGCCTAAAACATAACCCAAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGTGAGTACATTATATATACAGCTTTGGCATGGAGGAATAGGTCTTTTGGTT
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
agaagtgagttttaaaataatagtccttat------tgcgggttcaattatcagcaatatttgttttatgggtggtggctgattgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
| | | | || ||| | || |||||| ||| || | | | |||||| | || || ||||| ||| ||| | |||| ||| ||||||||| | ||||| |||| ||||||||| ||||| ||||| || ||||| |||||||| | ||||||||||||||||| |||||||| |
---actttttctctaagaggcagtgcatagaatatgtgcgggctcagttttt--ttgttgtcacattatggttaatgactt-ttgtttttttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagcaatatttgttttatgggtggtggctgattgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
tgttgat putative branch site (score: 4)
tttcattt CT-rich tract
ttgatttcatttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaagtgagttttaaaataatagtccttattgcgggttcaattatcagcaatatttgttttatgggtggtggctgattgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgatt