Sequence
atgc intronic sequence ATGC exonic sequencegtcatttccttttctgatagtagtgctagaatacgtcaaagaatattggtctaggattgaactacgcattggcaaactatggggattgatagattgatttgtttaatgttaccattttcatgaaagttttttccccaatgcagGATGCTGCTGCATGGCTTGAGTATTTTGAATCAAAAGCCCTAGAGCAGCAAGAAGCAGCTAAAAATGGAACTCCAAAGCCTGATGCATCCATTGCAAGTA
Basic information
species | Glycine max |
transcript | GLYMA08G22850.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G22850.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os04g55230.1 (Oryza sativa), 3'ss of exon 20
gtcatttccttttctgatagtagtgctagaatacgtcaaagaatattggtctaggattgaactacgcattggcaaactatggggattgatagattgatttgtttaatgttaccattttcatgaaagttttttccccaatgcagGATGCTGCTGCATGGCTTGAGTATTTTGAATCAAAAGCCCTAGAGCAGCAAGAAGCAGCTAAAAATGGAACTCCAAAGCCTGATGCATCCATTGCAAGTA
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-------------------------------------------gttttttttcccttcaaaatatgcaatgacgagtc-caaatactgctatgttctcttgg--actattaga-----catgataatttt---cctgctgcagGATGCTGCTGCATGGCTTGAGTATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCCGCCCGAAGGGGCATCCCAAAACCTGACTCATCTATTGCAAGCA
upper sequence: GLYMA08G22850.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM5G892758_T01 (Zea mays), 3'ss of exon 3
gtcatttccttttctgatagtagtgctagaatacgtcaaagaatattggtctaggattgaactacgcattggcaaactatggggattgatagattgatttgtttaatgttaccattttcatgaaagttttttccccaatgcagGATGCTGCTGCATGGCTTGAGTATTTTGAATCAAAAGCCCTAGAGCAGCAAGAAGCAGCTAAAAATGGAACTCCAAAGCCTGATGCATCCATTGCAAGTA
| | || || || | |||| | | | ||||| | || | | | || | | ||||||||||||||||||||||| || |||||||| |||||||| |||| || ||||| || || || || | ||||| |||||| |||| ||||||||||
-------------------------------------------------------------gttctttttctcagcgtacaaaaac--ataggatatatactccgatgttctc-ttgaattaacacattacttttcgatgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCTGCCCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTA
upper sequence: GLYMA08G22850.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G086030_T01 (Zea mays), 3'ss of exon 20
gtcatttccttttctgatagtagtgctagaatacgtcaaagaatattggtctaggattgaactacgcattggcaaactatggggattgatagattgatttgtttaatgttaccattttcatgaaagttttttccccaatgcagGATGCTGCTGCATGGCTTGAGTATTTTGAATCAAAAGCCCTAGAGCAGCAAGAAGCAGCTAAAAATGGAACTCCAAAGCCTGATGCATCCATTGCAAGTA
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------------------------------------------------------------gttcttttttcagggcatataaaaat--ataggatatatactctgatcttctc--ttgaattaacacattattgttgttgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTA
upper sequence: GLYMA08G22850.1 (Glycine max), 3'ss of exon 19
lower sequence: AT1G15290.1 (Arabidopsis thaliana), 3'ss of exon 18
gtcatttccttttctgatagtagtgctagaatacgtcaaagaatattggtctaggattgaactacgcattggcaaactatggggattgatagattgatttgtttaatgttaccattttcatgaaagttttttccccaatgcagGATGCTGCTGCATGGCTTGAGTATTTTGAATCAAAAGCCCTAGAGCAGCAAGAAGCAGCTAAAAATGGAACTCCAAAGCCTGATGCATCCATTGCAAGTA
| | | || | | || | || || | ||| | | | | ||| || | | | | ||||| || | | |||| | | | | ||| || | ||| | |||||||||||||||||||| || ||||||||||||| |||| |||||||||| ||||||| |||||||| |||||||||||||| ||||| || || |
----gtgattgatttgcttctggttc----attcgcatacaaatctcagacgaatatt-aatttcttactagcaaagtaacaaagtgaacgttttgaactctgagacat--acatgtttgttttctccatttgtctctcacagGATGCTGCTGCATGGCTCGAATATTTTGAATCAAGAGCCATAGAGCAGCAGGAAGCAGGCCGAAATGGAATCCCAAAGCCTGATGCTTCCATCGCGAGCA
upper sequence: GLYMA08G22850.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv09s0002g07530.t01 (Vitis vinifera), 3'ss of exon 20
gtcatttccttttctgatagtagtgctagaatacgtcaaagaatattggtctaggattgaactacgcattggcaaactatggggattgatagattgatttgtttaatgttaccattttcatgaaagttttttccccaatgcagGATGCTGCTGCATGGCTTGAGTATTTTGAATCAAAAGCCCTAGAGCAGCAAGAAGCAGCTAAAAATGGAACTCCAAAGCCTGATGCATCCATTGCAAGTA
|| || | || ||| ||| | | || | | | | | || |||| || | | || | || || | | || | | | |||||||||||||||||||||||||| ||||||||||||||||| ||||||||||||||||||| | |||||||||||||||||| |||||||| |||||||| |
------------------------------atgcgaccaa-----ttgagctaagggcatgtttagc--taatacaatgtcactatagatacataaaat-----ggagtcatcaattg-acgggcgtgtgtgttctcatgcagGATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAAGAAGCAGCAAGAAATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCA
upper sequence: GLYMA08G22850.1 (Glycine max), 3'ss of exon 19
lower sequence: EFJ08067 (Selaginella moellendorffii), 3'ss of exon 20
gtcatttccttttctgatagtagtgctagaatacgtcaaagaatattggtctaggattgaactacgcattggcaaactatggggattgatagattgatttgtt-taatgttaccattt-tcatgaaagttttttccccaatgcagGATGCTGCTGCATGGCTTGAGTATTTTGAATCAAAAGCCCTAGAGCAGCAAGAAGCAGCTAAAAATGGAACTCCAAAGCCTGATGCATCCATTGCAAGTA
||||| || | | | | || || | | ||||| | | | | | | | |||||||||||||| |||||||| |||||||| || ||||| | ||||| |||||||| | | | || | || ||||||||| | || ||||||| |
------------------------------------------------------------------------------------gttgatcgactccctcttgattgtgaaacagtctctcatgcatgatatgtgttctttacagGATGCTGCTGCCTGGCTTGATTATTTTGATTCTAAAGCAGTTGAGCAACAAGAAGCCACAAGGACAGGGGCACCTAAGCCTGATCCTTCTGTTGCAAGCA
upper sequence: GLYMA08G22850.1 (Glycine max), 3'ss of exon 19
lower sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 20
gtcatttccttttctgatagtagtgctagaatacgtcaaagaatattggtctaggattgaactacgcattggcaaactatggggattgatagattgatttgtt-taatgttaccattt-tcatgaaagttttttccccaatgcagGATGCTGCTGCATGGCTTGAGTATTTTGAATCAAAAGCCCTAGAGCAGCAAGAAGCAGCTAAAAATGGAACTCCAAAGCCTGATGCATCCATTGCAAGTA
||||| || | | | | || || | | ||||| | | | | | | | |||||||||||||| |||||||| |||||||| || ||||| | |||||||||||||| | | | || | || ||||||||| | || ||||||| |
------------------------------------------------------------------------------------gttgatcgactccctcttgattgtgaaacagtctctcatgcatgatatgtgttctttacagGATGCTGCTGCCTGGCTTGATTATTTTGATTCTAAAGCAGTTGAGCAGCAAGAAGCCACAAGGACAGGGGCACCTAAGCCTGATCCTTCTGTTGCAAGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagattgatttgtttaatgttaccattttcatgaaagttttttccccaatgcagGATGCTGCTGCATGGCTTGAGTATTTTGAATCAAAAGCCCTAGAGCAGCAAGAAGCAGCTAAAAATGGAACTCCAAAGCCTGATGCATCCATTGCAAGTA
gtttaat putative branch site (score: 4)
ttttttcccc putative PPT
atttgtttaatgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcatttccttttctgatagtagtgctagaatacgtcaaagaatattggtctaggattgaactacgcattggcaaactatggggattgatagattgatttgtttaatgttaccattttcatgaaagttttttccccaatgcagGATGCTGCTGCATGGCTTGAGTATTTTGAATCAAAAGCCCTAGAGCAGCAAGAAGCAGCTAAAAATGGAACTCCAAAGCCTGATGCATCCATTGCAAGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT