Sequence
atgc intronic sequence ATGC exonic sequence...gttgggcataggctggtcatcatagtttatggtgtaatgctcttgttttgtcttttgtgtggtgcaatgttcataactatttgtttttccaatggcccagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGTCGTCTTACCCTGAGGGAGCTGAAACGTGGAAACATAATTGATGCAAT
Basic information
species | Glycine max |
transcript | GLYMA19G43790.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 6
gttgggcataggctggtcatcatagtttatggtgtaatgctcttgttttgtcttttgtgtggtgcaatgttcata-actatttgtttttccaatggc--ccagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGTCGTCTTACCCTGAGGGAGCTGAAACGTGGAAACATAATTGATGCAAT
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-tgaggattctacgattggacctggtcaatgac-tattggtagtgatttgctggatgcctg-catctcattcatctgctaatcgtttattatgtaattttcagCTGAGACTGTAATATACAGAATCTTTTATTCCATAAATAGAGCTGGAAATGGCCATCTTACCCTCAGAGAGCTAAAACGTGGGAATTTAATTGCTGCGAT
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 6
gttgggcataggctggtcatcatagtttatggtgtaatgctct---tgttttgt-cttttg-tgtggtgcaatgt-tcataactatttgtttttccaatggcccagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGTCGTCTTACCCTGAGGGAGCTGAAACGTGGAAACATAATTGATGCAAT
| || || | |||| | | || || ||||||| || ||| | || ||| ||| | |||| || | | |||| || ||||| ||||||||||| | ||||| ||| |||||||| || ||||||| ||| || ||||| ||||| ||||||||||| |||||| |||| |
-----aactcaactatctattttgttttaagatcagatttgctgaatgttttgaactgttgctaatgtttgctgtgtcacattcatttcttgatgttttc-ttcagCGGAGACTGTAATATACAGAATCTTTTACTCCATAAATAGATCTGGGAATGGTCATCTGACTCTGAGAGAGCTCAAACGTGGAAATTTAATTGCTGCACT
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------------------------------------------------gttgggcataggctggtcatcatag---tttatggtgtaatgctct---tgttttgtcttttgtgtggtgcaatgttcataactatttgtttttccaatggcc-cagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGTCGTCTTACCCTGAGGGAGCTGAAACGTGGAAACATAATTGATGCAAT
| | | || | | | | | | || || ||| | ||| || | | || | || ||| | |||||| | |||| ||||||||||||| ||||||||||||||||||||||| ||||| |||||||| | ||||||| |||| ||||| || || ||||| || |||| |||||
gttagtgcaagaatatgaagtgatctttagttcggtttgtttttttacagttttgctgaaatagtaagatatgtttacattagatagaacaaaaatctaaaatgagatgtggtgaatgtaaagttgagtatatgatccattgta---atgtatttgaaaaacttttggcaacagCTGAAACTGTAATATACAGAATATATTACTACATAAATAGGAGTGGAAATGGGCATCTTACCTTGAGAGAGCTTAAGCGAGGAAATTTAGTTGACGCAAT
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 5
gttgggcataggctggtcatca--tagtttatggtgtaatgctcttgttttgtcttttg-tgtggtgcaatgttcata-actatttgtttttccaatggcccagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGTCGTCTTACCCTGAGGGAGCTGAAACGTGGAAACATAATTGATGCAAT
| | | || | | ||||||| | | ||| | | || || ||| | | | | || ||||| ||| ||| ||||||||||||||| |||||||||| ||||||||| |||||||| || |||||||| |||| | |||||||| ||||| |||||| |||||||||| ||
---gaaaaaaaaaaaatctggagcttgtttatgaatcatgtattttgatgaaacagctgatgctatgctacatgctgatacaatttgcatttt-gatgaaacagCTGAAACTGTCACCTACAGAATATTTTACTACATAAATAGATCTGGCAATGGTCGAATTACATTTAGGGAGCTTAAACGGGGAAACTTAATTGATGCTAT
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 6
-----gttgggcataggctggtcatcatagtttatggtgtaatgctcttgttttgtcttttgtgtggtgcaatgttcataactatttgtttttccaatggcccagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGTCGTCTTACCCTGAGGGAGCTGAAACGTGGAAACATAATTGATGCAAT
| || |||| | | | ||| | | |||| | | || | ||| || |||||| ||| || ||||||||||||||| ||| |||||| ||| ||||| |||||||| || |||||||| |||| | |||||||| ||||| |||||| |||||||||| ||
tctggagtccatattctttggtatttgctgctaccggtatcaaagctaaatttt----taaggatgcttttctgtctgatacaatttgtatttt-gctgaaacagCTGAAACTGTCACCTACCGAATATTTTATTACATAAATAGATCTGGCAATGGTCGAATTACATTTAGGGAGCTTAAACGGGGAAACTTAATTGATGCTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgtcttttgtgtggtgcaatgttcataactatttgtttttccaatggcccagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGTCGTCTTACCCTGAGGGAGCTGAAACGTGGAAACATAATTGATGCAAT
tcataac putative branch site (score: 2)
tttttcca putative PPT
ataactatttgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgggcataggctggtcatcatagtttatggtgtaatgctcttgttttgtcttttgtgtggtgcaatgttcataactatttgtttttccaatggcccagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGTCGTCTTACCCTGAGGGAGCTGAAACGTGGAAACATAATTGATGCAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - taggctg
- - - - - - - - - - - - - - - - -gtaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgtt