Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttttctggatagaaattttgtaagtaatttcttaggccgttgaataatctgagtgggaaactgtgtcaaattgtgcctgaattatgaaattttcttatctttaactcttttctcataatcaaaattttcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAG
Basic information
species | Glycine max |
transcript | GLYMA15G01680.1 |
intron # | 9 |
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 9
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 9
gtaagttttttctggatagaaattttgtaagtaatttcttaggccgttgaataatctgagtgggaaactgtgtcaaattgtgcctgaattatgaaattttcttatctttaactc--ttttctcataatcaaaattttcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAG
| ||| | || | | || | || | |||| | || | | || || | ||| | ||| ||| | | | |||||||||||| || ||||||||||| ||||| ||| | ||| |||| || ||||| ||||| ||||||||||||| |||||| ||||| || ||||| ||
----------------------------------------------caatttgctcttcacagaaacccttttcttttcatgttttcatta----acttcttccttttcaagttaatttagtgatacgggaaaaaacttg----acttgtgcagGGTTGTGATCGGATATGATGAAGGGACAATAATGATAAAAATTGGCCGTGAAGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAA
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 9
gtaagttttttctggatagaaattttgtaagtaatttcttaggccgttgaataatctgagtgggaaactgtgtcaaattgtgcctgaattatgaaattttcttatctttaactcttttctcataatcaaaattttcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAG
| | |||| | | | | | | | |||| || || || || | | | || || || || | || || | ||| | || | ||||| | | | ||| | || ||||| |||||||| ||||| || ||| | ||| | || || |||||||||||||| |||||||| | |||||| ||||| |||||| | ||
-----------gtaaacagaagatccttt-gcattctgcttttgtgttgcatt------gtaatcaattgcttttactactg------ttctgcgtcactcctcctttcaattttttaacaccattcgacattttatgatatgt------agGATGGTAATTGGTTATGATGAGGGAACTATAATGATAAAAATGGGACGTGAAGTACCTGTGGCAAGCATGGATACCAGTGGAAAAATCATTTGGGCAAAA
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 9
gtaagttttttctggatagaaattttgtaagtaatttcttaggccgttgaataatctgagtgggaaactgtgtcaaattgtgcctgaattatgaaattttcttatctttaactcttttctcataatcaaaattttcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAG
| ||||||| | ||||| || | ||||| | ||| | ||| || | |||| | | | || | ||| || ||||| || | |||||||||||||| ||||||||||| ||||| ||| | ||| ||||||| ||||| ||||| ||||||||||| | |||||| |||||||| ||| | |||
-----------------------------aagaatttctc---tcattgaaacatgt-----------tgtgtgagattttcattgacttgtt---ctttcctgcataagtcaagttaatgatatggaatattttattttgtgt------agGGTTGTGATTGGATATGATGAAGGGACAATAATGATAAAAATTGGTCGTGAAGTTCCTGTTGCTAGCATGGATAGCAGTGGAAAAATTATATGGGCAAAG
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 9
gtaagttttttctggatagaaattttgtaagtaatttcttaggccgttgaataatctgagtgggaaactgtgtcaaattgtgcctgaattatgaaattttct-tatctttaactcttttctcataatcaaaattttcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAG
|| | | | || | | ||||| | ||| | | | || ||| || || | | || | ||| ||| || | ||| | ||||||||||||| || |||||||| ||||| ||| | ||| ||||||| ||||| ||||| ||||||||||| | |||||| |||||||| ||| | |||
-------------------------------------------taaagatatgttatcactgaaaca-tgtgtgagatttttaattggct-tgttctttcctgcataagtcaagctaatggcatggaaaaacttattttgtgta--------gGGTTGTGATTGGATACGATGAAGGGACAATAATGATAAAAATTGGTCGTGAAGTTCCTGTTGCTAGCATGGATAGCAGTGGAAAAATTATATGGGCAAAG
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 10
gtaagttttttctggatagaaattttgtaagtaatttcttaggccgttgaataatctgagtgggaaactgtgtcaaattgtgcctgaattatgaaattttcttatctttaactcttttctcataatcaaaattttcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAG
|| | ||| | | || | || || || ||| | ||| || || || | ||||| |||| || |||||||| ||||| ||||||||||| ||| | || |||| || |||| |||||| ||||| ||||| | |||||| ||||| || ||| | ||
---------------------------------------------------------------------gtattaaaaaa-acttagtttcttgttttctccaattggtaagtgtttacttg-----aatatatca------attcatacagAGTCGTGATTGGATATGACGAAGGAACAATAATGATTAAGATTGGGCGTGAAGCACCTGTTGCTAGTATGGATAGCAGTGGTAAAATCATATGGGCCAAA
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagttttttctggatagaaattttgtaagtaatttcttaggccgttgaataatctgagtgggaaactgtgtcaaattgtgcctgaattatgaaattttcttatctttaactcttttctcataatcaaaattttcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAG
||||| | | ||| | || || | | | || | | || | || || | || ||| || | | | ||| || | ||||||||||||| || |||||||||||||| || ||||| |||||||| |||||| | ||||| |||||||||||||| | || ||||| || ||| |||||
-------------------------------------cttagatttgttagaaatgatattgagagg-tctacctggttctag-tactccattgagttgtcctgca---aaaccttaccttgt---ccacattctca-------tttcacagGGTTGTGATCGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAATACCGGAAAAATCATATGGGCTAAG
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaagttttttctggatagaaattttgtaagtaatttcttaggccgttgaataatctgagtgggaaactgtgtcaaattgtgcctgaattatgaaattttcttatctttaactcttttctcataatcaaaattttcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAG
|||||||| ||| | | ||| | || || | | || || | | | | | |||| | || | | || || | || ||| | ||| || ||| | || | || ||||||||| ||||| ||||| |||||| | || ||||| |||||||| || ||| |||| |||||||| ||||| ||||| || |||||||||||| ||||
gtaagttt---ctgatcttttactatgtcaatatttattcc--ctattaaagatatatatcttcacatcat----aattatttctttgt-gtaaatttatgtttccttcataacttacgagatgg-caatacctt-----gtctttttccagGGTTGTAATTGGTTATGACGAAGGATCCATAATGGTGAAACTTGGCCGTGAAATACCAGTGGCTAGTATGGATAACAGCGGAAAAATTATTTGGGCTAAA
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaagttttttctggatagaaattttgtaagtaatttcttaggccgttgaataatctgagtgggaaactgtgtcaaattgtgcctgaattatgaaattttcttatctttaactcttttctcataatcaaaattttcgggtgcattcaa---acagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAG
| | |||||| | || | || | | | | | | || ||| |||| | | | || | || || || |||||||||||||||| |||||||||||||| || ||||| |||||||| |||||| | ||||| ||||||||||||| || || ||||| || ||| |||||
-----------------------------------------------agggcgtttagagtggctaggagtttt---ttagggatcagtgttagcaccttatta-----aactgatcatacgggaccatcaacaacgaatgtgtttgctttacagGGTTGTGATTGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAG
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 9
gtaagttttttctggatagaaattttgtaagtaatttcttaggccgttgaataatctgagtgggaaactgtgtcaaattgtgcctgaattatgaaattttcttatctttaactcttttctcataatcaaaattttcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAG
| | | | | |||| | || || | | | | | | || || ||| || | || | || ||| | ||| | | | || ||||||||| || |||||||||||||||| |||||||| ||||||||| ||||||| |||||||| || |||||||||||||| ||||| || ||| |||||
----------------------tgtcacacttcacttctcttgttcctg--tagccagcactaaatatt--------tagtatatggcttaggaga-------------aa----tggcttggaatgactattattgc---tctccatccagGGTTGTAATCGGCTATGATGAAGGAAGTATTATGGTAAAACTTGGTAGAGAAGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAG
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 9
gtaagttttttctggatagaaattttgtaagtaatttcttaggccgttgaataatctgagtgggaaactgtgtcaaattgtgcctgaattatgaaattttcttatctttaactcttttctcataatcaaaattttcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAG
|| || ||| ||||||||| | | ||| | |||| | | || |||| ||| | | | | || ||| || ||| | | | || ||||||||||||| || | |||||||||||| |||||||| ||| |||||||||| | ||| || ||||| ||||| || ||||| || || || ||| ||||
---------------------------aaaatataggttta---ttttgaataatt--gttatcacactctctcaa--tatagttgctgtatg--ctttattcacatgtggcttctttttc----------tttcc---tacttt---acagGGTTGTGATCGGTTTTGATGAAGGAACCATTATGGTGAAAATTGGTCGAGATGAACCAGTAGCTAGTATGGATAATAGTGGAAAGATCATATGGGCTAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcttatctttaactcttttctcataatcaaaattttcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAG
ctttaac putative branch site (score: 3)
ttttctcataatcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttttttctggatagaaattttgtaagtaatttcttaggccgttgaataatctgagtgggaaactgtgtcaaattgtgcctgaattatgaaattttcttatctttaactcttttctcataatcaaaattttcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA