Sequence
atgc intronic sequence ATGC exonic sequence...ttggaatattcaaatattgcatcatgagtcatgctgcatgacatgaatcacggcatcattttgaggggtttcttttttctttctatctttctttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC
Basic information
| species | Glycine max |
| transcript | GLYMA07G05660.1 |
| intron # | 1 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G05660.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g02300.1 (Oryza sativa), 3'ss of exon 1
----------------------------------------ttggaatattcaaatattgcatcatgagtc-atgctgcatgacatgaatca--cggcatcattttgaggggt----ttcttttttctttctatct-ttctttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC
| ||| |||| | | | | || ||| || || || ||||| || | | | | || | | | | | ||| | || | ||||||||| || || || || | |||||||| || |||||||||||||||||||| |||||||||||||| || || ||| | || || | || || ||
gtagctaagctagtattcctcatcatataacctttctcctctccaattctcaatttctagctaccaaatcgatgatggatt-tatcaatcaatcgagctaagctagctaagtaatggtgtgtgtgcaaaatatatattgtggttgcagAGAGGTGTAAGATTGGGTCAGGGCCGCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACAGGGCGACGGC
upper sequence: GLYMA07G05660.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g04090.1 (Oryza sativa), 3'ss of exon 1
ttggaatattcaaatattgcatcatgagtcatgctgcatgacatgaatcacggcatcattttgaggggtttcttttttcttt-ctatctttctttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC
|| || || || || | || || | | ||| |||||| | | | | | | || | | |||||||| |||| || || | ||||| || || |||||||||||||||||||| |||||||||||||| || || ||| | || || || || || ||
-----gtacgtaattaagcacacacacatcgatcaattcgat-cgatttttgacat-gttttgatcaatgtggcatgtgtgtatcatacatacatatgcagAGAGGTGCAGGATTGGGTCAGGGCCGCAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACCGGGCAACGGC
upper sequence: GLYMA07G05660.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G171395_T01 (Zea mays), 3'ss of exon 1
----------------------------------ttggaatattcaaatat-tgca-tcatgagt-catgctgcatgacatgaatcacggcatcattttgaggggtttcttttttctttctatctttctttt------tgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC
||| || || | | ||| |||| | ||||| | || | | || | | || | | || || | | ||||||||| ||| || || | || ||||| || |||||||||||||||||||| |||||||||||||| || || ||||||||||| |||||||| ||
gtagtactacgctgttacgcacgcacgcgcttgcttgctgcatacatgtctatgcggccatgcatacatgcctc-tgccgtccgtctgccctccccgatgcatatatggccgatcctgatcgtcgagccggtgaccgatgcagAGAAGTGCCGCATCGGTTCGGGCCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACCGC
upper sequence: GLYMA07G05660.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
ttggaatattcaaatattgcatcatgagtcatgctgcatgacatgaatcacggc-atcattttgaggggtttcttttttctttctatctttctt-tttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC
| || ||| |||| | | | || | | | || | | | | | | | || ||| | || | |||||||||||||| || || | ||| ||||| || |||||||||||||||||||| |||||||||||||| || || ||||||||||| |||||||| ||
atcaaacgcgatcgaatt-catcgcgcgcta-actactggctaacaactgctactactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
upper sequence: GLYMA07G05660.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G069047_T01 (Zea mays), 3'ss of exon 1
------------------------------------------------------------------ttggaat--attcaaatattgcatcatga--gtcatgctgcatga-catgaatcacggc--atcat------tttgaggggtttctt-------ttttctttctatctttctttt-tgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC
| | || || | | | | ||| |||||| || || |||||| || ||||| | || | | | || | || || | | | |||||||| |||||| || || | ||| ||||| || |||||||||||||||||||| |||||||||||||| || || ||||||||||| ||||| || ||
gtacggtatacttaccaccatataccttccatctccgaggtccgagcaaagcatcagctcgtgatcataggatcggatcggagctggtgacctgatggtcatgtcacacgagcatgaacgtgagctgatcatcgtacgtccatggcgctgatcatcggggttagttatcgattctgcgtgcatgcagAGAGATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCTACGGC
upper sequence: GLYMA07G05660.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
-------------------ttggaatattcaaatattgcat---catgagtcatgctgcatgacatgaatcacggcatcattttgaggggttt-cttttttctttctatctttctttttgcagAGAAATGCAAAATAGGAACCAC------TCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC
| | || | | || ||||| |||| | || ||| | || || | | || | | | | |||||| || ||| | || | | || ||||| || |||||||||||||||||||| |||| ||||||||| || || ||||||||||| |||||
gtatgcatccatgcatatagtaggatctgtgtacgagacacatgcatga-tcatcgtctatctcattgcttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcagACAAGTGCCGCGTCGGGTCGTCGTCAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC------
upper sequence: GLYMA07G05660.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0048g02660.t01 (Vitis vinifera), 3'ss of exon 1
---------------------------ttggaatattcaaatattgcatcatgagtcatgctgcatga--catgaatcacggcat-cattttgaggggtttcttttttctttctatctttctttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC
| | | || | | | || || || || ||| || | || | || || | | | || | || | ||||||||||||| || | ||||||| |||| || || || ||||||||||||||||||||||| |||||||| || || || ||||| | || ||||||||||||||
gttgtgcttcatatttagttcatcgcctctcattcttttctcttaattttgcaattcttgttgaatattccatcaag-atagcgtgtatcttcccctttgtgatgttcatatcggcttgggtttttgcagAGAAGTGTAGAATAGGATCCACCCCTCAAAACGATTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCAACGGGAACCAGGACTAATCGCGCCACTGC
upper sequence: GLYMA07G05660.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S1_447V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------------------------------------------------ttggaatattcaaatattgca-tcatgagtcatgctgcatgacatgaatcacggcatcattttgaggggtttcttttttctttctatctttctttttg-------cagAGAAATGCAAAATAGGAACCACTCCGC---------AGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC
|| | | | || |||| | ||||| || | | | | || | ||| | | | | | | | || |||| |||| || || | || | | || || |||||||||||||||||||||||||| ||||||||| | || | || | || ||
gtaagaatcgatcagaatcctcggtgtactatgtatgacaccagactagaaaacacgtcctcacatgcttcgttgccccatttcagtctattaagattgaactcatgg--tgtgttcgagccctgggattgcaattagattccatgtccactacgtacacggacaagtaaccccgatgtggtcatcagAAGTGTGCAGGATTGGGGACGACCCACCAGAGAATCAAAACGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCCTCGGGCAATCGAGCGAACCG---------
upper sequence: GLYMA07G05660.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S182_37V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------------------------------------------ttggaatatt-caaatattgcatcatgagtcatgctgcatgacatgaatcacggcatcattttgaggggtttcttttttctttctatctttctttttgcagAGAAATGCAAAAT-AGGAACCACTCCGCAGAA--------TGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC
||| | | | || || ||| ||| |||| | | | | |||| | | | | || | || | |||| |||| || || || || | |||| ||| |||||||||||||||||||| || |||||||| |||||||||| || |||| ||
gtaagcatcggaatcctgaaggtagtatggtgcagtgttcaacctcctcatctagtttcgtcaaaaaataaacatttaaaacagtactatccattgaattgtgatcaacataagctcaagag-catgttctcctcatctattgatagcatgaaatggtccagcagtattgacaaaaacttgttgcaccgatcagAAGTGTGCAGGATCGGGGACGACGCACCAGAGCATCAAAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAGTATCCCACAGGAAACCGTGCCAACCG---------
upper sequence: GLYMA07G05660.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
ttggaatattcaaatattgca-tcatgagtcatgctgcatgacatgaat-cacggcatcattttgaggggtttcttttttctttctatct-----ttctttttgcagAGAAATGCAAAAT----AGGAACCACTCCG-----CAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC
| || || ||| | | || ||| | || || || || | || | | | || || ||| || |||||||| |||||| || | |||| |||| ||||| | ||||||||||| ||||| || ||||||||||||||||| || | ||| |||| ||
-------gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
upper sequence: GLYMA07G05660.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
--------------ttggaatattcaaatattgcatcatgagtcatgctgcatgacatgaatcacggcatcattttgaggggtttcttttttctttctatctttctttt------tgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC
|| ||| || | | | | | | | || | | || | | | | | || | | | || | ||| |||| ||| ||| || || | |||| | || ||||||||||||||||||||||||||||| ||||| || || ||| | ||||| | ||||| |
gtaagacggtcatccctcaagcttctcatttcggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: GLYMA07G05660.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ22020 (Selaginella moellendorffii), 3'ss of exon 1
ttggaatattcaaatattgcatcatgagtcatgctgcatgacatgaatcacggcatcattttgaggggtttcttttttctttctatctttctttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC
| | | |||| | || ||| | || | ||| ||| | | |||| || | | |||| |||||||| || || || ||| | || || | || |||||||| ||||| ||||| ||||||||||| ||||| ||||| |||||||| | ||||| ||
------------------gtagtct-agtc-tcctccatttcg-atatgattgcacaccactgaca-----cctctttcattgttcttcgattttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC
upper sequence: GLYMA07G05660.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
-----ttgg--aatattcaaatattgcatcatgagtcatgctgcatgacatgaatcacggcat--cattttgaggggtttcttttttctttctatc------tttctttt------tgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC
|| | |||| | ||| | | | | | | | | | || | | | | | | | | | ||| || | ||| |||| ||| ||| || || | |||| | || ||||||||||||||||||||||||||||| ||||| || || ||| | ||||| | ||||| |
gtaagacggtcatccctcaagcttctcatttcgggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: GLYMA07G05660.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ18283 (Selaginella moellendorffii), 3'ss of exon 1
ttggaatattcaaatattgca-tcatgagtcatgctgcatgacatgaatcacggcatcattttgaggggtttcttttttctttctatctttctttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC
| | || | || | | ||||||| | || || || | | | | |||| || | | |||| |||||||| || || || ||| | || || | || |||||||| ||||| ||||| ||||||||||| ||||| ||||| |||||||| | ||||| ||
------------------gtagtctagtctcctccatttcgacatga-ttaca-caccact-------gacacctctttcattgttcttcgattttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcacggcatcattttgaggggtttcttttttctttctatctttctttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC
tttcttttttctttct CT-rich tract
tttcttttttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttggaatattcaaatattgcatcatgagtcatgctgcatgacatgaatcacggcatcattttgaggggtttcttttttctttctatctttctttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - tattgca
- - - - - - - - - - -tcatgag
- - - - - - - - - - - - - - tcatgct
- - - - - - - - - - - - - - - - - -gcatgac
- - - - - - - - - - - - - - - - - - - - - - - - cacggca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgagggg
