Sequence
atgc intronic sequence ATGC exonic sequencegtgatgattttttttgctcagtagctaagataattgatgagtagtgcatgtaattaattaatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
Basic information
species | Glycine max |
transcript | GLYMA19G44890.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g04090.1 (Oryza sativa), 3'ss of exon 1
-----------------------gtgatgattttttttgctcagtagc-taagataattgatgagtagtgcatgtaattaattaatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
||| | || | | | | | | | || ||| | || |||| | | | |||||||| ||||| || || | || |||||||| |||||||| |||||||||||||||||||||||||| ||||| | | || ||||| || |
gtacgtaattaagcacacacacatcgatcaattcgatcgatttttgacatgttttgatcaatgtggcatgtgtgtatcatacatacatatgcagAGAGGTGCAGGATTGGGTCAGGGCCGCAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACCGGGCAACGGC
upper sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g02300.1 (Oryza sativa), 3'ss of exon 1
-----------------------------------------------------------------------gtgatgattttttttgctcagt-agctaagataattgatgagtagtgcatgt---aattaattaatttg--tgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
||||| ||| | | ||||||| || | | | | ||| ||| || || || | || |||||||| ||| || || || | || || ||||| |||||||| |||||||||||||||||||||||||| ||||| | | || ||| | || |
gtagctaagctagtattcctcatcatataacctttctcctctccaattctcaatttctagctaccaaatcgatgatggatttatcaatcaatcgagctaagctagctaagtaatggtgtgtgtgcaaaatatatattgtggttgcagAGAGGTGTAAGATTGGGTCAGGGCCGCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACAGGGCGACGGC
upper sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G171395_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------gtgatgattttttttgctcagtagctaagata-attgatgagtagtgcatgtaattaat----taatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
|| | | | | ||| || ||| | | | | | | | |||||||| |||| || || |||| || ||||| |||||||| |||||||||||||||||||||||||| ||||| | |||||||||||||||| |
gtagtactacgctgttacgcacgcacgcgcttgcttgctgcatacatgtctatgcggccatgcatacatgcctctgccgtccgtctgccctccccgatgcatatatggccgatcctgatcgtcgagccggtgaccgatgcagAGAAGTGCCGCATCGGTTCGGGCCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACCGC
upper sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
------------------------gtgatgattttttttgctcagtagctaagataattgatg--agtag-tgcatgtaattaattaa---tttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
| | | | | | || |||| | | | | | ||| | ||| || || | | ||||||| ||||| || || | || || ||||| |||||||| |||||||||||||||||||||||||| ||||| | ||||||||||||||||
atcaaacgcgatcgaattcatcgcgcgctaactactggctaacaactgctactactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
upper sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G069047_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------------------------------------------------------------gtgatgattttttttgctcagtagctaagataattgatgagtagtgcatgtaattaattaatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
| | |||| | | || | || ||| || | | |||| | | | | | |||||||| ||||| || || | || || ||||| |||||||| |||||||||||||||||||||||||| ||||| | |||||||||||||| |
gtacggtatacttaccaccatataccttccatctccgaggtccgagcaaagcatcagctcgtgatcataggatcggatcggagctggtgacctgatggtcatgtcacacgagcatgaacgtgagctgatcatcgtacgtccatggcgctgatcatcgg-ggttagt---tatcgattctgcgtgcatgcagAGAGATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCTACGGC
upper sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------gtgatgat--tttttttgctcagtagctaagataattgatgagtagtgcatgt-----aattaattaatttgtgcagAGATGTGCAAAATAGGA-----AGCAG-CCCACAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
|||| || | | | | | | || | ||| |||| | |||| | | | | |||||| | |||| | || ||| ||| || ||||| |||||||| |||||||||||||||| ||||||||| ||||| | ||||||||||||||
gtatgcatccatgcatatagtaggatctgtgtacgagacacatgcatgatcatcgtctatctcattgcttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcagACAAGTGCCGCGTCGGGTCGTCGTCAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC------
upper sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------gtgatgattttttttgctcagtagctaagataattgatgagtagtgcatgtaattaattaatttg----tgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
| ||| ||| | || | || | | | || | || | || ||||||| || | ||| || | ||||||||||| |||||||| ||||||||||||||||||||||| || || || | | | || ||||| || | |
gttaaaccctaaatatgaaaaaaaactctttcatttctacgaactctctatttctttgttctttatttttgaaccattttggtatgcaaatgcagAGGAATGTAGAATCGGTTCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
upper sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G46770.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------gtgatgattttt--tttgctcagtagctaagata--attgatgagtagtgcatgtaattaattaatttgt---gcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
|| | | |||| | | || || || ||| | | | | | | | |||| || | || ||||||||||| |||||||||| | ||||||||||| ||||| || || |||||||||||||| || || || ||||||| | || ||| | ||||
catattcggagttagttactgcaaagaccaacataggtttggttattatacaatttactatttaagtttttttcttctgattatttttgtcgttatgcagAGATGTGTAAAATAGGAACAACGCCACAAAACGACTGGTATTTCTTTAGCCACAAGGACAAAAAATATCCGACGGGAACGAGAACTAACAGAGCCACTGC
upper sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G61910.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------------gtgatgattttttttgctcagtagctaagat-aattgatgagtagtgcatgtaattaattaatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
||||| || |||| ||||| | || | | | | || || | || || | | || ||||||||| || || |||| | || ||||||||||||||||| | ||||| |||||||||||||| ||||| || | | |||||| | |||| ||
caggaaattttgcagagtaatatatactttttgtgataataaaatttg--cagtaacaaaattcagtcaaaacttaacacaactc-ttgttttttctatgtagAGATGTGTAAGATTGGAACGACGCCGCAAAACGATTGGTACTTTTATAGCCATAAGGACAAGAAGTATCCCACCGGGACTAGAACCAACAGAGCCACCAC
upper sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S1_447V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------------------------------------------------------------------------gtgatgattttttttgctcag-tagctaagataattgatgagtagtgcatgta--attaattaatt----tgtg-----cagAGATGTGCAAAATAGGAAGCAGCCCAC---------AAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
|| || || || | | || | | | | ||| | | | | | || ||| |||| |||| |||||| || || | ||||| ||||||| |||||||| ||||||||||| ||||| ||||||||| |||| | || | |||||
gtaagaatcgatcagaatcctcggtgtactatgtatgacaccagactagaaaacacgtcctcacatgcttcgttgccccatttcagtctattaagattgaactcatggtgtgttcgagccctgggattgcaattagattccatgtccactacgtacacggacaagtaaccccgatgtggtcatcagAAGTGTGCAGGATTGGGGACGACCCACCAGAGAATCAAAACGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCCTCGGGCAATCGAGCGAACCG---------
upper sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S182_37V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------------------------------------------------------------------------gtgatgattttttttgctcagtagctaagataattgatgagtagtgcatgtaattaattaatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCAC---------AAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
|| | | | | | | | | || | | |||| || || | || | |||| |||||| || || | | ||| ||| || |||||||| |||||||||||||| |||||||| ||||| |||| ||| |||||||
gtaagcatcggaatcctgaaggtagtatggtgcagtgttcaacctcctcatctagtttcgtcaaaaaataaacatttaaaacagtactatccattgaattgtgatcaacataagctcaagagcatgttctcctcatctattgatagcatgaaatggtccagcagtattgacaaaaacttgttgcaccgatcagAAGTGTGCAGGATCGGGGACGACGCACCAGAGCATCAAAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAGTATCCCACAGGAAACCGTGCCAACCG---------
upper sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------gtgatgattttttttgctca-gtagctaagataatt----gatgagtagtgcatgtaattaattaat------ttgtgcagAGATGTGCAAAATAGGAAGCAGCCCA---------CAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
||| | | | | | |||| || ||||| || | ||| | || ||||||| | ||||| || | || || || ||| | |||||||| || ||||| |||||||||||||||||||| || | |||| |||||||
gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
upper sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ22020 (Selaginella moellendorffii), 3'ss of exon 1
gtgatgattttttttgctcagtagc--taagataattgatgagtagtgcat-----gtaattaattaatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
| | | | | ||| | | || ||| | | | | | | || | |||| ||||||| ||| || || ||| ||||| ||| |||||||| ||||| ||||||||||||||||| |||||||||| ||||||||| | |||| |
---gtagtctagtctcctccatttcgatatgattgcacaccactgacacctctttcattgttcttcgattttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC
upper sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ18283 (Selaginella moellendorffii), 3'ss of exon 1
-----gtgatgattttttttgctcagtagcta-agataattgatgagtagtgcatgtaattaattaatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
| | | || | | || | | | ||| | | ||| || | |||| ||||||| ||| || || ||| ||||| ||| |||||||| ||||| ||||||||||||||||| |||||||||| ||||||||| | |||| |
gtagtctagtctcctccatttcgacatgattacacaccactgacacctctttcatt--gttcttcgattttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctcagtagctaagataattgatgagtagtgcatgtaattaattaatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
aattaat putative branch site (score: 3)
atgtaattaattaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatgattttttttgctcagtagctaagataattgatgagtagtgcatgtaattaattaatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT