Sequence
atgc intronic sequence ATGC exonic sequencegtgatgatttttttgctaagtagctaagataattaatgagtagtgcatgtaattgattaatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGTACAAGAAGTACCCCACGGGAAGCCGCACAAACCGCGCCACCAG
Basic information
species | Glycine max |
transcript | GLYMA19G44910.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G44910.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g04090.1 (Oryza sativa), 3'ss of exon 1
--------------------gtgatgatttttttgctaagtagctaaga-----taattaatgagtagtgcatgtaattgattaatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGTACAAGAAGTACCCCACGGGAAGCCGCACAAACCGCGCCACCAG
||| || | | | | | | | || |||| | || |||| | | | |||||||| ||||| || || | || |||||||| |||||||| |||||||||||| ||||||||||||| ||||| | | || ||||| || ||
gtacgtaattaagcacacacacatcgatcaattcgatcgatttttgacatgttttgatcaatgtggcatgtgtgtatcatacatacatatgcagAGAGGTGCAGGATTGGGTCAGGGCCGCAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACCGGGCAACGGC
upper sequence: GLYMA19G44910.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g02300.1 (Oryza sativa), 3'ss of exon 1
-----------------------------------------------------------------------gtgatgatttttttgctaagt--agctaagataattaatgagtagtgcatgt---aattgattaatttg--tgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGTACAAGAAGTACCCCACGGGAAGCCGCACAAACCGCGCCACCAG
||||| ||| | | | | ||||||| || ||| | | ||| ||| || | || | || |||||||| ||| || || || | || || ||||| |||||||| |||||||||||| ||||||||||||| ||||| | | || ||| | || ||
gtagctaagctagtattcctcatcatataacctttctcctctccaattctcaatttctagctaccaaatcgatgatggatttatcaatcaatcgagctaagctagctaagtaatggtgtgtgtgcaaaatatatattgtggttgcagAGAGGTGTAAGATTGGGTCAGGGCCGCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACAGGGCGACGGC
upper sequence: GLYMA19G44910.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G171395_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------gtgatgatttttttgctaagtagctaagataattaatgagta-gtgcatgtaattgat-----------taatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGTACAAGAAGTACCCCACGGGAAGCCGCACAAACCGCGCCACCAG
| || | ||| || | ||| || || | |||| | | |||||||| |||| || || |||| || ||||| |||||||| |||||||||||| ||||||||||||| ||||| | ||||| ||||||||||||
gtagtactacgctgttacgcacgcacgcgcttgcttgctgcatacatgtctatgcggccatgcatacatgcctctgccgtccgtctgccctccccgatgcatatatggccgatcctgatcgtcgagccggtgaccgatgcagAGAAGTGCCGCATCGGTTCGGGCCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACCGC
upper sequence: GLYMA19G44910.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
------------------------gtgatgatttttttgcta--agtagctaagataattaatg--agtag-tgcatgtaat---tgattaatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGTACAAGAAGTACCCCACGGGAAGCCGCACAAACCGCGCCACCAG
| | | | | | |||| | |||| | | ||| | ||| | ||| || || | | ||||||| ||||| || || | || || ||||| |||||||| |||||||||||| ||||||||||||| ||||| | ||||| |||||||||||
atcaaacgcgatcgaattcatcgcgcgctaactactg-gctaacaactgctactactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
upper sequence: GLYMA19G44910.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G069047_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------------------------------------------------------gtgatgatttttttgctaagtagctaagataattaatgagtagtgcatgtaattgatta---atttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGTACAAGAAGTACCCCACGGGAAGCCGCACAAACCGCGCCACCAG
||| | | | | | | || | | | || || |||| | |||||||| ||||| || || | || || ||||| |||||||| |||||||||||| ||||||||||||| ||||| | ||||| |||||||| ||
gtacggtatacttaccaccatataccttccatctccgaggtccgagcaaagcatcagctcgtgatcataggatcggatcggagctggtgacctgatggtcatgtcacacgagcatgaacgtgagctgatcatcgtacgtccatggcg-ctgatcatcggggttagttatcgattctgcgtgcatgcagAGAGATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCTACGGC
upper sequence: GLYMA19G44910.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
------------------------------------------------gtgatgatttttttgctaagtagctaagataattaatgagtagtgcatgt-----aattgattaatttgtgcagAGATGTGCAAAATAGGA-----AGCAG-CCCACAAAACGATTGGTACTTGTTCAGCCACAAGTACAAGAAGTACCCCACGGGAAGCCGCACAAACCGCGCCACCAG
| || | | | | | | || | ||| |||| | |||| | || | | |||||| | |||| | || ||| ||| || ||||| |||||||| |||||||||||| ||| ||||||||| ||||| | ||||| ||||||||
gtatgcatccatgcatatagtaggatctgtgtacgagacacatgcatgatcatcgtctatctcattgcttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcagACAAGTGCCGCGTCGGGTCGTCGTCAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC------
upper sequence: GLYMA19G44910.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
------------------------gtgatgatttttttgctaagtagctaaga--taattaatgagtagtgcatgtaattgattaatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGTACAAGAAGTACCCCACGGGAAGCCGCACAAACCGCGCCACCAG
| ||| | | || | ||| | || | | | || | ||| | ||||||| || | ||| || | ||||||||||| |||||||| |||||||||||| |||||||||| || || || | | | || ||||| || ||
gttaaaccctaaatatgaaaaaaaactctttcatttctacgaactctctatttctttgttctttatttttgaaccattttggtatgcaaatgcagAGGAATGTAGAATCGGTTCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
upper sequence: GLYMA19G44910.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G46770.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------gtgatgatttttttgctaagtagctaagata--attaatgagtagtgcatgtaattgattaatttgt---gcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGTACAAGAAGTACCCCACGGGAAGCCGCACAAACCGCGCCACCAG
| || |||| | | || || || ||| | | | | | | | ||| || | || ||||||||||| |||||||||| | ||||||||||| ||||| || || ||||||||| |||| || || || ||||||| | || ||| | |||||
catattcggagttagttactgcaaagaccaacataggtttggttattatacaatttactatttaagtttttttcttctgattatttttgtcgttatgcagAGATGTGTAAAATAGGAACAACGCCACAAAACGACTGGTATTTCTTTAGCCACAAGGACAAAAAATATCCGACGGGAACGAGAACTAACAGAGCCACTGC
upper sequence: GLYMA19G44910.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S1_447V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------------------------------------------------gtgat-gatttttttgct---aagtagctaagataattaatgagta---gtgcatgtaatt--gattaatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCAC---------AAAACGATTGGTACTTGTTCAGCCACAAGTACAAGAAGTACCCCACGGGAAGCCGCACAAACCGCGCCACCAG
||| | || | | | || ||| | || | | ||| | || |||| ||| | | |||| |||||| || || | ||||| ||||||| |||||||| ||||||||||| |||| ||||||||| |||| | || | |||||
gtaagaatcgatcagaatcctcggtgtactatgtatgacaccagactagaaaacacgtcctcacatgcttcgttgccccatttcagtctattaagattgaactcatggtgtgttcgagccctgggattgcaattagattccatgtccactacgtacacggacaagtaaccccgatgtggtcat-cagAAGTGTGCAGGATTGGGGACGACCCACCAGAGAATCAAAACGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCCTCGGGCAATCGAGCGAACCG--------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctaagtagctaagataattaatgagtagtgcatgtaattgattaatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGTACAAGAAGTACCCCACGGGAAGCCGCACAAACCGCGCCACCAG
gattaat putative branch site (score: 3)
atgtaattgattaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatgatttttttgctaagtagctaagataattaatgagtagtgcatgtaattgattaatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGTACAAGAAGTACCCCACGGGAAGCCGCACAAACCGCGCCACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT