Sequence
atgc intronic sequence ATGC exonic sequence...atgttctccactcatacatgagagaaagtcactgatattgctaactcgacaagtatattaattcagatatttgcaatatgatatttgttgtcttccatagGATTCGAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGGCAAGCTCGTAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC
Basic information
species | Glycine max |
transcript | GLYMA19G39300.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G39300.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g71200.1 (Oryza sativa), 3'ss of exon 5
atgttctccactcatacatgagagaaagtcactgatattgctaactcgacaagtatattaattcagatatttgcaatatgatatttgttg---tcttccatagGATTCGAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGGCAAGCTCGTAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC
| | | ||| | | | || | | || || ||| | | ||| || || | | ||| || | | || | || |||| || ||||| || || |||||||||||||| ||||| |||||||||||||| || || | ||| || || || || | ||| | |||||| | ||
-gataccttgtgtctgcattatattat-ccagttacatccctt-ctcaaaccccacgttatttttcatgaatatattataatctcttctgatttatttgttagGGCTCTAGTGTGCCGTTGGTTGTCAAATGGGCCGATACAGAAAAGGAAAGGCAGGCCCGAAAAGCACAAAAGGCTCAATTGCAATCATCTAATATGCCTA
upper sequence: GLYMA19G39300.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g30980.1 (Oryza sativa), 3'ss of exon 5
----atgttctccactcatacatgagagaaagtcactgatattgctaactcgacaagtatattaattcagatatttgcaatatgatatttgttg-tcttccatagGATTCGAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGGCAAGCTCGTAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC
| | || | | || | | | | ||| | || | | | | | | || | | |||| | || |||| |||| ||| ||||| || || ||||| ||||||||||| ||||| |||||||| |||||||| | ||| || || || || | || | |||||| | ||
agccagctccttaagttgtatt---aatatattagctgtttcctttatgtt--tgaattttcacagttgattacatagatcttgatgtgccctgatcttttgtagGGTTCAAGTGTACCTTTGGTTGTTAAATGGGCTGACACTGAGAAGGAAAGACAAGCTCGAAAAGCACAAAAGGCTCAATTTCACCCATCTAATATGTCAA
upper sequence: GLYMA19G39300.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G128809_T01 (Zea mays), 3'ss of exon 6
atgttctccactcatacatgag----agaaagtcac-tgatattgctaactcgacaagtatattaattcagatatttgcaatatgatatttgttgtcttccatagGATTCGAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGGCAAGCTCGTAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC
| || | |||| | | | ||| |||||| | | ||| || | | | ||| || | || ||| || || | || |||| ||| ||||||||||| ||||||||||||||||| ||||||||||||||||||||||| | ||| || ||| | | | ||| ||||||| |
taatagatcattgataccttggccttgtatagttgtatgatatagattactt--cagttctgaaatctcatgaatct--aacatggc-ttggtcattttggttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAAGCTCGAAAAGCGCAAAAATCTCCATTCCAGTCTTCTAACATGTTGA
upper sequence: GLYMA19G39300.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G177001_T01 (Zea mays), 3'ss of exon 5
atgttctccactcatacatgagagaaagtcactgatattgctaactcgacaagtatatta--attcagatatttgcaatatgatatttgttgtcttccatagGATTCGAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGGCAAGCTCGTAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC
|| | | | | | | | | | |||| | || || | || | | | | | | | || ||| | || | || |||| ||| ||||||||||| ||||||||||||||||| ||||||||||||||||| ||||| | ||| || ||||| || | ||| ||||||| |
atatcattgataccttggtcttgtatgat-attgatcacttcagttctgaaatttcatgaccagttacacaaatctaacatgcc-ctggtcatttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA
upper sequence: GLYMA19G39300.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G005459_T01 (Zea mays), 3'ss of exon 5
--atgttctccactcatacatgagagaaagtc--actgatattgctaactcgacaagtatattaattcagatatttgcaatatgatatttgttgtcttccatagGATTCGAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGGCAAGCTCGTAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC
| | ||| | | | ||| ||| || | ||| | | | | || | | || ||| ||||| ||| || | | | | || |||| ||| || || || || |||||||||||||||||||| |||||||||||||| ||||| | ||| || ||||| ||||| || ||| || ||||
taaagctcttctttttttcattttagacagcccatttgacacttattatatgaacattgtacatattt-gatatcc-caac--gagctctaatatattttgtagGGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGGCAGGCTCGGAAAGCACAAAAAGCTCAGTCACAGCTATCTCATATACCCA
upper sequence: GLYMA19G39300.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0104g01150.t01 (Vitis vinifera), 3'ss of exon 5
atgttctccactcatac-atgagagaaagtcactgatattgctaactcgacaagtatattaattcagatatttgcaatatgatatttgttgtcttcca---tagGATTCGAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGGCAAGCTCGTAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC
|| ||| | | | | | || ||| | || | | || |||| ||| | || ||| || | ||| |||| ||| |||||||| |||||||||||||||||||||||||||||||||| |||||||| | ||||||||||| || || || || |||||| | |||
----tccccagttctgtgaagtgggatagtggatttctgccttataaaaatggagaagttgattcgatgattggttatctgaccattagtttctgttgcattagGGTTCAAGTGTTCCTCTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGGAAGGCTCAGAAAGCTCAATCTCAGGCATCTAATTTGCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgacaagtatattaattcagatatttgcaatatgatatttgttgtcttccatagGATTCGAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGGCAAGCTCGTAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC
tattaat putative branch site (score: 2)
ttgtcttcc putative PPT
aagtatattaattcag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgttctccactcatacatgagagaaagtcactgatattgctaactcgacaagtatattaattcagatatttgcaatatgatatttgttgtcttccatagGATTCGAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGGCAAGCTCGTAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - -ccactca
- - - - - - - -acatgag
- - - - - - - - - - - - - -gtcactg
- - - - - - - - - - - - - - - - - - - tgctaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgcaa