Sequence
atgc intronic sequence ATGC exonic sequencegtagttcaattatatcaacatatttactagtatggtagagcttatgcatgatataaagtaaattttcatcctcttgcagCCTAAGCTGTTGGATGAGAAGCAGACAACTATCTATAAGAGGGCTGTTGACAAGAGTTATCACTTGAAGATGAAAGCGTCTAGGTTCATTTTCAGTGAAA
Basic information
species | Glycine max |
transcript | GLYMA16G19310.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G19310.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g28280.1 (Oryza sativa), 3'ss of exon 6
gt-agttcaattatatcaacatatttactagtatggtaga-gcttatgcatgatataaagtaaattttcatcctcttgcagCCTAAGCTGTTGGATGAGAAGCAGACAACTATCTATAAGAGGGCTGTTGACAAGAGTTATCACTTGAAGATGAAAGCGTCTAGGTTCATTTTCAGTGAAA
|| || | | | | | | || | | |||| | | || | | || | | ||||| ||| | ||||||||||||||||| || ||||| ||||| ||||| ||||||| ||||||||||||||||||||| |||||||||||||||||||| |
gtgagaatagctgcttttatttgaaggattgtcttctgtttgctttttttttttacatttttttttaattacgacgcacagCCCAAGTTATTGGATGAGAAGCAGACCACCATCTACAAGAGAGCTGTAGACAAGAATTATCACTTGAAGATGAAAGCATCTAGGTTCATTTTCAGTGAGA
upper sequence: GLYMA16G19310.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G133884_T01 (Zea mays), 3'ss of exon 2
---------------gtagttcaattatatcaacatatttactagtatggtagagcttatgcatgatataaagtaaattttc-----atcctcttgc-agCCTAAGCTGTTGGATGAGAAGCAGACAACTATCTATAAGAGGGCTGTTGACAAGAGTTATCACTTGAAGATGAAAGCGTCTAGGTTCATTTTCAGTGAAA
| | | || | ||| | || | ||| | | | |||||| || || ||| |||| ||| | ||||||||||||||||| |||||||| || | || ||| ||||||| |||| |||||||||||||||| || ||||| |||||||||||||
atgtgtttctacgtttttagtaagaaattctgttttttttttgcatgtgatgcttcttttttccatgtctgatcacattttcgtagaatattcatgccagCCCAAGTTATTGGATGAGAAGCAGACCACTATCTACAAAATGGTTGTAGACAAGAATTATAACTTGAAGATGAAAGCATCAAGGTTTATTTTCAGTGAAA
upper sequence: GLYMA16G19310.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G388234_T01 (Zea mays), 3'ss of exon 2
gtagttcaatt-atatcaacatatttactagtatggtagagcttatgcatgatataaagtaaattttcatcctcttgc-agCCTAAGCTGTTGGATGAGAAGCAGACAACTATCTATAAGAGGGCTGTTGACAAGAGTTATCACTTGAAGATGAAAGCGTCTAGGTTCATTTTCAGTGAAA------
||| | || | | || | | | | ||| |||| | | | || || || ||| | || ||| | ||||||||||||||||| |||||||| || |||||||| ||||||| ||| || ||||||||||||| || | ||| |||||||||||||
gtaagaaattttgtttttttgcatgtgatgcttcttttttttccatgtatgac-cacattttcgttgaatattcatgccaacccaagTTATTGGATGAGAAGCAGACCACTATCTACAAAAGGGCTGTAGACAAGAACTATAACCTGAAGATGAAAGCATCAACGTTTATTTTCAGTGAAATCAGCC
upper sequence: GLYMA16G19310.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G440820_T01 (Zea mays), 3'ss of exon 1
----------------gtagttcaattatatcaacatatttactagtatggtagagcttatgcatgatata-aagtaaattttc-----atcctcttgc-agCCTAAGCTGTTGGATGAGAAGCAGACAACTATCTATAAGAGGGCTGTTGACAAGAGTTATCACTTGAAGATGAAAGCGTCTAGGTTCATTTTCAGTGAAA-
| || | | || | ||| | | || | ||| | || | | | |||||| || || ||| |||| ||| | ||||||||||| |||| |||||||| || |||||||| ||||||| ||| || |||| |||||||| || ||||| ||||||| |||||
ccagcactggggaggggaaggtaagaaattcttttttttttgc--atgtgatgcttctttttttccatgtctgaccacattttcgttgaatattcatgccagCCCAAGTTATTGGATGAGAA-TAGACCACTATCTACAAAAGGGCTGTAGACAAGAACTATAACCTGAAAATGAAAGCATCAAGGTTTATTTTCAATGAAAT
upper sequence: GLYMA16G19310.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S119_137V6.1 (Physcomitrella patens), 3'ss of exon 5
---------gtagttcaattatatcaacatatttactag---tatggtagagcttatgcatgatataaagtaaattttcatc---------ctcttgcagCCTAAGCTGTTGGATGAGAAGCAGACAACTATCTATAAGAGGGCTGTTGACAAGAGTTATCACTTGAAGATGAAAGCGTCTAGGTTCATTTTCAGTGAAA
| || ||| | ||| | ||| | ||| | || | | | | || |||| | || ||||||| |||||| |||| ||||||||||| || | || ||||||||||| ||||||| ||| || | |||||||| ||||| || |||||||| |||||||
ccactgcaaatgattgccttagagggtcattgtgactgaatctgccgtaaatgccatttagattgtgacgttcttttttgttgttacctttctgctgcagCCAAAGCTGCTGGACGAGAAGCAGACCACGGTGTACAAGAGGGCTGTGGACAAGAATTACCATCTCAAGATGAAGGCGTCAAGATTCATTTTTAGTGAAA
upper sequence: GLYMA16G19310.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S264_34V6.1 (Physcomitrella patens), 3'ss of exon 5
---------gtagtt-caattatatca---acatatttactagtatggtagagcttatgcatgat-ataaagtaaat-tttcatc------ctcttgcagCCTAAGCTGTTGGATGAGAAGCAGACAACTATCTATAAGAGGGCTGTTGACAAGAGTTATCACTTGAAGATGAAAGCGTCTAGGTTCATTTTCAGTGAAA
|| || | |||| || | ||| | | | || | | || || || | ||| ||||||| | ||||||| ||| |||| |||||||||||||| || | |||||||||||||| ||||||| ||||||| |||| ||||| || || || ||||| ||||| ||||
taccttcatttaattataggtatagcagatagttatctttgaacttaactgaagtccttcaggaccatggcattaatgtttcatcactgttccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGACAAGAATTATCACCTGAAAATGAAGGCATCAAGATTCATCTTCAGCGAAA
upper sequence: GLYMA16G19310.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ35350 (Selaginella moellendorffii), 3'ss of exon 5
gtagttcaattatatcaacatatttactagtatggtagagcttatgcatgatataaagtaaattttcatcctcttgcagCCTAAGCTGTTGGATGAGAAGCAGACAACTATCTATAAGAGGGCTGTTGACAAGAGTTATCACTTGAAGATGAAAGCGTCTAGGTTCATTTTCAGTGAAA
| | ||| | | | || | | | | ||| || | ||| |||||| ||||| | || |||| |||||||| |||| || ||||| || |||||||| ||||| ||||||||||| || || ||||| || ||||||||||
-------------gtttgtagctttgacttatcgttgaaatctaaggaagtaagaaacgcaaacgttatc-----gcagCCGAAGCTTCTCGACGAGAGACAGACAACAGTCTACAAAAGGGCCGTGGACAAGAGCTATCATTTGAAGATGAAGGCCTCGAGGTTTATATTCAGTGAAA
upper sequence: GLYMA16G19310.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ10608 (Selaginella moellendorffii), 3'ss of exon 5
gtagttcaattatatcaacatatttactagtatggtagagcttatgcatgatataaagtaaattttcatcctcttgcagCCTAAGCTGTTGGATGAGAAGCAGACAACTATCTATAAGAGGGCTGTTGACAAGAGTTATCACTTGAAGATGAAAGCGTCTAGGTTCATTTTCAGTGAAA
|| || ||| | | | | || | || ||| ||| | || | ||||| ||||| | || |||| |||||||| |||| || ||||| || |||||||| ||||| ||||||||||| || || ||||| || ||||||||||
------------gttcgtagctttgacttat-cgttgaaatcta---acgaagtaag--aaacgcaaacgctatcacagCCGAAGCTTCTCGACGAGAGACAGACAACAGTCTACAAAAGGGCCGTGGACAAGAGCTATCATTTGAAGATGAAGGCCTCGAGGTTTATATTCAGTGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactagtatggtagagcttatgcatgatataaagtaaattttcatcctcttgcagCCTAAGCTGTTGGATGAGAAGCAGACAACTATCTATAAGAGGGCTGTTGACAAGAGTTATCACTTGAAGATGAAAGCGTCTAGGTTCATTTTCAGTGAAA
ttttcatcctcttgc CT-rich tract
atgatataaagtaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttcaattatatcaacatatttactagtatggtagagcttatgcatgatataaagtaaattttcatcctcttgcagCCTAAGCTGTTGGATGAGAAGCAGACAACTATCTATAAGAGGGCTGTTGACAAGAGTTATCACTTGAAGATGAAAGCGTCTAGGTTCATTTTCAGTGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG