Sequence
atgc intronic sequence ATGC exonic sequencegtattacatatgatttgatagctaatcttaattccatttttcctgactgcatattatctatagcataaattccatgattttttcaatctcaccagcgatctatatatggtgacaatcagttaacttggttatttctggtagaacagTTTATCATGTATTAAGGGGTACAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGACGGAGGATTTGCTCCCAATGTTCAAGATAACAGGAGG
Basic information
species | Glycine max |
transcript | GLYMA15G25390.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G25390.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g20820.1 (Oryza sativa), 3'ss of exon 2
gtattacatatgatttgatagctaatcttaattccatttttcctgactgcatattatctatagcataaattccatgattttttcaatctcaccagcgatctatatatggtgacaatcagttaacttggttatttctggtagaacagTTTATCATGTATTAAGGGGTA----CAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGACGGAGGATTTGCTCCCAATGTTCAAGATAACAGGAGG
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------------------------acattggcaacagttacatctgc-gcatttgacttgtagtttgctctc----gtcttttaattctca-----aatgtttgtcttctgaga-----tttacctgtccatgtt-------acagTTTACCATGCCCTAAAGGGCATCATTAAGGCGAAATATGGTCAAGATGCATGCAATGTTGGAGATGAAGGTGGCTTTGCTCCTAATGTTCAAGACAACAG----
upper sequence: GLYMA15G25390.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G034848_T01 (Zea mays), 3'ss of exon 2
gtattacatatgatttgatagctaatcttaattccatttttcctgactgcatattatctatagcataaattccatgattttttcaatctcaccagcgatctatatatggtgacaatcagttaacttggttatttctggtagaacagTTTATCATGTATTAAGGGGTA----CAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGACGGAGGATTTGCTCCCAATGTTCAAGATAACAGGAGG
||| | | | | | | ||||||| ||| | || ||| | || || | ||| | || | || | | ||||| |||| |||||||| ||||| | | ||| | |||||||||||||| ||||||||||| ||||| |||||||| ||||| |||||||| ||||||||||| |||||
------------------------------------tttgttataaaagtaaac-atctatatttgggattt--ttgcttcttctagctggtcacttcatcttctatcctcact-tggaatatccttgttat----ggta--acagTTTACCATGTCCTGAAGGGCATCATTAAGGCAAAATATGGTCAAGATGCATGCAATGTCGGAGATGAAGGAGGTTTTGCTCCTAATGTTCAAGACAACAG----
upper sequence: GLYMA15G25390.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 2
gtattacatatgatttgatagctaatcttaattccatttttcctgactgcatatta-tctatagcataaattccatgattttttcaatctcaccagcgatctatatatggtgacaatcagttaacttggttat-ttctggtagaacagTTTATCATGTATTAAGGGGTA----CAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGACGGAGGATTTGCTCCCAATGTTCAAGATAACAGGAGG
| ||| | | ||||| | | | |||| | || | | | | || | | || ||| || | | |||||||| |||||||| ||||| | | | | | ||| |||||||||| ||||||||||| ||||| |||||||| ||||| |||||||| ||||||||||| |||||
--------------------------------------------tatgttgtatcagtgaatagctatattgggactatttgcttctgctagctggtcactt-catcttctaacc-tcacttggaatatccttgttctggta--acagTTTACCATGTCCTGAAGAGCATCATTAAGTCAAAATATGGTCAAGATGCATGCAATGTCGGAGATGAAGGAGGTTTTGCTCCTAATGTTCAAGACAACAG----
upper sequence: GLYMA15G25390.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 2
gtattacatatgatttgatagctaatcttaattccatttttcctgactgcatattatctatagcataaattccatgattttttcaatctcaccagcgatctatatatggtgacaatcagttaacttggttatttctggtagaacagTTTATCATGTATTAAGGGGTA----CAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGACGGAGGATTTGCTCCCAATGTTCAAGATAACAGGAGG
| | | | | | || ||| ||| ||| || || || | | | | ||| | | | | | || || | |||||||||||| ||| | ||| | ||| | || ||||| |||||||| |||||||| |||||||| ||||| ||||| || |||||||||||||||||
---------------------------------------------catatttctcttttggttccaaagttcttctattctttggattatcacaaagaattgtttttc-tgatagtaatgcatttaatgtactttgttgattacagTTTATCATACATTGAAGGGGATAATCAAAACTAAGTATGGTCAAGATGCTTGTAATGTCGGAGATGAAGGAGGGTTTGCGCCGAATGTTCAAGATAACAG----
upper sequence: GLYMA15G25390.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 2
gtattacatatgatttgatagctaatcttaattccatttttcctgactgcatattatctatagcataaattccatgattttttcaatctcaccagcgatctatatatggt--gacaatcagttaacttggttatttctggtagaacagTTTATCATGTATTAAGGGGTA----CAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGACGGAGGATTTGCTCCCAATGTTCAAGATAACAGGAGG
|| ||| | | | ||| ||| |||| || | || | | | ||| ||| ||| | || | | |||| || | || | ||||||||||| | | | ||| | ||||||||||||||||||||||||||| |||||||| ||||| || |||||||||||||||||||| ||||| ||
--------------------------------------ttctatgattatgcagt-tctttagt--------tgtgatattgttgatgcaataatccatc-ataaatgataggaaagataaataaccatttttaatttgtgggggcagTTTATCATACACTGAAGGGAATTATCAAGGCAAAATATGGACAAGATGCATGCAATGTTGGGGATGAGGGGGGATTTGCTCCCAATGTTCAGGATAATAG---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccagcgatctatatatggtgacaatcagttaacttggttatttctggtagaacagTTTATCATGTATTAAGGGGTACAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGACGGAGGATTTGCTCCCAATGTTCAAGATAACAGGAGG
agttaac putative branch site (score: 3)
atctatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattacatatgatttgatagctaatcttaattccatttttcctgactgcatattatctatagcataaattccatgattttttcaatctcaccagcgatctatatatggtgacaatcagttaacttggttatttctggtagaacagTTTATCATGTATTAAGGGGTACAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGACGGAGGATTTGCTCCCAATGTTCAAGATAACAGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT