Sequence
atgc intronic sequence ATGC exonic sequencegtaagacgactcattacagagaaatattttcagcgaaaggaagactatctggttatgtagaaacatgtatttgctgactaaagtgcaattgaacagatggcttgatctctgttcttgttctctgcagaaaagcaaaataaagcctgttcatgttgttgatgttcctggtcatgcagGGCTCAAACCCAAGCTTGATGAAGTCCTGCCTCAAGCAGCTGGGATAGTTTTTGCTGTTGATGCTCAAGATTTCTTGTCCACCATGCAAGTCGTTGCAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os06g27870.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g27870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G059260_T01 (Zea mays), 3'ss of exon 3
gtaagacgactcattacagagaaatattttcagcgaaaggaagactatctggttatgtagaaacatgtatttgctgactaaagtgcaattgaacagatggcttgatctctgttcttgttctctgcagaaaagcaaaataaagcctgttcatgttgttgatgttcctggtcatgcagGGCTCAAACCCAAGCTTGATGAAGTCCTGCCTCAAGCAGCTGGGATAGTTTTTGCTGTTGATGCTCAAGATTTCTTGTCCACCATGCAAGTCGTTGCAGA
|| | | | | || | | | | || || | ||||||| || | |||||| | || | | ||||| | ||| ||||||||| ||| |||| | ||| |||||| ||||||||||||||||||| ||||||||||||| |||||||||||||||||| ||| ||| | || |
-------------------agttctgctagtaatgtaaatagttttgtttc-ttgtgaaaaaacatgcatatcctgactgcgatatttctgctaaacc-------ttcctgttgtccttccctgcagAAAGAAAAAGTAAAACTTGTGCATGTTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGTTGCTACAGTTGTCT-------------------------------------------------
upper sequence: LOC_Os06g27870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G175054_T01 (Zea mays), 3'ss of exon 6
gtaagacgactcattacagagaaatattttcagcgaaaggaagactatctggttatgtagaaacatgtatttgctgactaaagtgcaattgaacagatggcttgatctctgttcttgttctctgcagaaaagcaaaataaagcctgttcatgttgttgatgttcctggtcatgcagGGCTCAAACCCAAGCTTGATGAAGTCCTGCCTCAAGCAGCTGGGATAGTTTTTGCTGTTGATGCTCAAGATTTCTTGTCCACCATGCAAGTCGTTGCAGA
|| | | | | || | | | | || || | ||||||| || | |||||| | || | | ||| || ||| | ||| ||||||||| |||| |||| ||||| |||||| ||||||||||||||||||| ||||||||||||| |||||||||||||||||| ||| |||| | | || |
-------------------agttctgctagtaatgtaaatagttttgtttc-ttgtgaaaaaacatgcatatcctgactgcgatatttctgc-taaac--cttcat----gttgtccttccctgcagAAAGACAAAGTAAAACCTGTGCATGTTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGTTGCTGCGGTTGTCT-------------------------------------------------
upper sequence: LOC_Os06g27870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G091503_T04 (Zea mays), 3'ss of exon 4
------------gtaagacgactcattacagagaaatattttcagcgaaagga---agactatctggtt----atgtagaaacatgtatttgctgactaaagtgcaattgaacagatggcttgatctctgttcttgttctctgcagaaaagcaaaataaagcctgttcatgttgttgatgttcctggtcatgcagGGCTCAAACCCAAGCTTGATGAAGTCCTGCCTCAAGCAGCTGGGATAGTTTTTGCTGTTGATGCTCAAGATTTCTTGTCCACCATGCAAGTCGTTGCAGA
|| | | || | ||||| || || | ||| | | ||| ||| | ||||||| || | |||||| | || | | ||||| | ||| ||||||||| |||| |||| ||||| ||| || ||||||||||||||||||| ||||||||||||| |||||||||||||||||| |||| |||| | | || |
gtatgcaaacttctagagctcattctttttccaacatattgagagaaaagtaatgtagatagttttgtttcttatgaaaaaacatgcatatcctgactgcgatatttctgctaaacc-------ttcctgttgtccttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGCTGCTGCGGTTGTCT-------------------------------------------------
upper sequence: LOC_Os06g27870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G014704_T01 (Zea mays), 3'ss of exon 1
---------gtaagacgactcattacagaga-aatattttcagcgaaaggaagactatctggttatgt---------agaaacatgtatttgctgactaaagtgcaattgaacagatggcttgatctctgttcttgttctctgcagaaaagcaaaataaagcctgttcatgttgttgatgttcctggtcatgcagGGCTCAAACCCAAGCTTGATGAAGTCCTGCCTCAAGCAGCTGGGATAGTTTTTGCTGTTGATGCTCAAGATTTCTTGTCCACCATGCAAGTCGTTGCAGA
| | ||||| || || || || |||| | | || | ||| ||| | ||||| | || | |||| | | || | | ||||| | ||| ||||||||| |||| |||| ||||| ||| || ||||||||||||||||||| ||||||||||||| |||||||||||||||||| |||| |||| ||| || |
gtatgcaaacttctagagttcattctttttccaacatattgagagaaaagtaatgtaaatagttttgtttcttgtgaaaaaacacgcatatcctgattgcgatatttctgctaaacc-------ttcctgttgtccttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGCTGCTGCGATTGTCT-------------------------------------------------
upper sequence: LOC_Os06g27870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G015642_T01 (Zea mays), 3'ss of exon 4
------------gtaagacgactcattacagagaaatattttcagcgaaaggaaga-------ctatctggttatgtagaaacatgtatttgctgactaaagtgcaattgaacagatggcttgatctctgttcttgttctctgcagaaaagcaaaataaagcctgttcatgttgttgatgttcctggtcatgcagGGCTCAAACCCAAGCTTGATGAAGTCCTGCCTCAAGCAGCTGGGATAGTTTTTGCTGTTGATGCTCAAGATTTCTTGTCCACCATGCAAGTCGTTGCAGA
|| | | || | ||||| | ||| |||| | | ||||| ||||||||| ||||||||||| ||||| | | | | | ||||| ||| |||||||| ||||| |||| ||||| ||| |||||||||||||||||||||| ||||||| |||||||||||||||||||||||| |||| |||||| | || |
gtatggaaacttctagagctcattctttttccaacatattgagataaaaatgaagtgaatagctttttctcttatgaagaaacatgcatttgctgact-----gcaatagttctgctaaacc--ttcctgttgcccttccgtgcagAAAGGCAAAGTAAAACCTGTGCATATTGTTGATGTTCCTGGTCATGCTAGGCTCAAGCCCAAGCTTGATGAAGTCCTGCCTAAAGCTGCTGGGGTTGTCT-------------------------------------------------
upper sequence: LOC_Os06g27870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G466947_T01 (Zea mays), 3'ss of exon 8
gtaagacgactcattacagagaaatattttcagcgaaaggaagactatctggttatgtagaaacatgtatttgctgactaaagtgcaattgaacagatggcttgatctctgttcttgttctctgcagaaaagcaaaataaagcctgttcatgttgttgatgttcctggtcatgcagGGCTCAAACCCAAGCTTGATGAAGTCCTGCCTCAAGCAGCTGGGATAGTTTTTGCTGTTGATGCTCAAGATTTCTTGTCCACCATGCAAGTCGTTGCAGA
|| | | | | || | | | | || || | |||||| || | |||||| | || | | ||||| | ||| ||||||||| |||| |||| ||| | |||||| ||||||||||||||||||| ||||||||||||| |||||||||||||||||| ||| |||| | | || |
-------------------agttctgctagtaatgtaaatagttttgtttc-ttgtgaaaaaacatccatatcctgactgcgatatttctgctaaacc-------ttcctgttgtccttccctgcagAAAGACAAAGTAAAACCTATGCATGTTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGTTGCTGCGGTTGTCT-------------------------------------------------
upper sequence: LOC_Os06g27870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G886354_T01 (Zea mays), 3'ss of exon 1
------------------gtaagacgactcattacaga--gaaatattttcagcgaaaggaagactatctggttatgtagaaacatgtatttgctgactaaagtgcaattgaacagatggcttgatctctgttcttgttctctgcagaaaagcaaaataaagcctgttcatgttgttgatgttcctggtcatgcagGGCTCAAACCCAAGCTTGATGAAGTCCTGCCTCAAGCAGCTGGGATAGTTTTTGCTGTTGATGCTCAAGATTTCTTGTCCACCATGCAAGTCGTTGCAGA
| | | | ||| | || | | | | || | ||| | || || | ||||||| || | |||||| || || | | | | | ||||| | ||| ||| ||||| |||| |||| ||||| ||| || ||||||||||||||||||| ||||||||||||| |||||||||||||||||| |||| ||| | | || |
gtatgcaaacttctggagttcattctttttccaacatattgagagaaaagtaatgtaaatagttttatttc-ttgtgaaaaaacatgcatatcctgact-----gcgatatttctgctagacc--ttcctgttgtccttccctgtagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGCTCCTGCGGTTGTCT-------------------------------------------------
upper sequence: LOC_Os06g27870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G701405_T01 (Zea mays), 3'ss of exon 1
---------gtaagacgactcattacagaga-aatattttcagcgaaaggaagactatctggttatgt---------agaaacatgtatttgctgactaaagtgcaattgaacagatggcttgatctctgttcttgttctctgcagaaaagcaaaataaagcctgttcatgttgttgatgttcctggtcatgcagGGCTCAAACCCAAGCTTGATGAAGTCCTGCCTCAAGCAGCTGGGATAGTTTTTGCTGTTGATGCTCAAGATTTCTTGTCCACCATGCAAGTCGTTGCAGA
| ||||| || || || || |||| | | || | ||| ||| | ||||||| || | |||||| | || | | ||||| | ||| || |||||| |||| |||| | ||| ||| || ||||||||||||||||||| ||||||||||||| |||||||||||||||||| |||| |||| | | || |
gtatgcaaacttctggagttcattctttttccaacatattgagagaaaagtaatgtaaatagttttgtttcttgtgaaaaaacatgcatatcctgactgcgatatttctgctaaacc-------ttcctgttgtccttccctacagAAAGACAAAGTAAAACATGTGCATATTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGCTGCTGCGGTTGTCT-------------------------------------------------
upper sequence: LOC_Os06g27870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G325453_T01 (Zea mays), 3'ss of exon 8
gtaagacgactcattacagagaaatattttcagcgaaaggaagactatctggttatgtagaaacatgtatttgctgactaaagtgcaattgaacagatggcttgatctctgttcttgttctctgcagaaaagcaaaataaagcctgttcatgttgttgatgttcctggtcatgcagGGCTCAAACCCAAGCTTGATGAAGTCCTGCCTCAAGCAGCTGGGATAGTTTTTGCTGTTGATGCTCAAGATTTCTTGTCCACCATGCAAGTCGTTGCAGA
|| | | | | || | | | | || || | ||||||| || | |||||| | || | | ||||| | ||| ||||||||| ||| |||| | ||| |||||| ||||||||||| ||||||| ||||||||||||| |||||||||||||||||| ||| |||| | | || |
-------------------agttctgctagtaatgtaaatagttttgtttc-ttgtgaaaaaacatgcatatcctgactgcgatatttctgctaaacc-------ttcctgttgtccttccctgcagAAAGATAAAGTAAAACTTGTGCATGTTATTGATGTTCCTAGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGTTGCTGCGGTTGTCT-------------------------------------------------
upper sequence: LOC_Os06g27870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G800070_T01 (Zea mays), 3'ss of exon 1
---------gtaagacgactcattacagaga-aatattttcagcgaaaggaagactatctggttatgt---------agaaacatgtatttgctgactaaagtgcaattgaacagatggcttgatctctgttcttgttctctgcagaaaagcaaaataaagcctgttcatgttgttgatgttcctggtcatgcagGGCTCAAACCCAAGCTTGATGAAGTCCTGCCTCAAGCAGCTGGGATAGTTTTTGCTGTTGATGCTCAAGATTTCTTGTCCACCATGCAAGTCGTTGCAGA
| ||||| || || || || |||| | | || | ||| ||| | ||||||| || | |||||| | | || | | ||||| | ||| ||||||||| |||| |||| ||| | ||| || ||||||||||||||||||| ||||||||||||| |||||||||||||||||| |||| |||| | | || |
gtatgcaaacttctggagttcattctttttccaacatattgagagaaaagtaatgtaaatagttttgtttcttgtgaaaaaacatgcatatcctgactgcaatatttctgctaaacc-------ttcctgttgtccttccctgcagAAAGACAAAGTAAAACCTATGCATATTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGCTGCTGCGGTTGTCT-------------------------------------------------
upper sequence: LOC_Os06g27870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G04110.1 (Glycine max), 3'ss of exon 3
gtaagacgactcattacagagaaatattttcagcgaaaggaagactatctggttatgtagaaacatgtatttgctgactaaa--gtgcaattgaacagatggcttgatctctgttcttgttctctgcagaaaagcaaaataaagcctgttcatgttgttgatgttcctggtcatgcagGGCTCAAACCCAAGCTTGATGAAGTCCTGCCTCAAGCAGCTGGGATAGTTTTTGCTGTTGATGCTCAAGATTTCTTGTCCACCATGCAAGTCGTTGCAGA
| | | | || ||| | | |||| | ||| | | | | |||||| | ||| | | | | | ||| | | ||||| |||| |||||||||||||||||||||||||||||||| ||| | |||| |||||| || ||||| | ||||||||||||||||| ||||||
----------------------------ctgaattatatcaatcttatttcat-atgtttgtttgttgattgtggaatcagacaatagaattgactaaatgttgtcttatatttctttgattttaacagAAGGGCAAGATAAAGCCTGTTCATGTTGTTGATGTTCCTGGGCATTCTCGGCTTCGACCCAAACTGGATGAGTACTTGCCTCAAGCAGCTGGGGTAGTTT-------------------------------------------------
upper sequence: LOC_Os06g27870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA01G03540.1 (Glycine max), 3'ss of exon 3
gtaagacgactcattacagagaaatattttcagcgaaaggaagactatctggttatgtagaaacatgtatttgctgactaaagtgcaattgaacagatggcttgatctctgttcttgttctctgcagaaaagcaaaataaagcctgttcatgttgttgatgttcctggtcatgcagGGCTCAAACCCAAGCTTGATGAAGTCCTGCCTCAAGCAGCTGGGATAGTTTTTGCTGTTGATGCTCAAGATTTCTTGTCCACCATGCAAGTCGTTGCAGA
| || | || || | || |||| | ||| ||| | |||| | || | | |||||| | ||| | | | | |||| | | ||||| |||| ||||| |||||||||||||||||||||||||| ||| | |||| |||||| || ||||| | ||||||||||||||||||||||||
---------------------agatgtctt-agtagctgaaattatatc-aatcgtgttt---catatgtttgtttg-tacaatagaattgagtaaatgttgtctaatatttccttgattttaacagAAGGGCAAGATAAAACCTGTTCATGTTGTTGATGTTCCTGGGCATTCTCGGCTTCGACCCAAACTGGATGAGTACTTGCCTCAAGCAGCTGGGATAGTTT-------------------------------------------------
upper sequence: LOC_Os06g27870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G05670.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaagacgactcattacagagaaatattttcagcgaaaggaagactatctggttatgtagaa-acatgtatttgctgactaaag-tgcaattgaacagatggcttgatc----tctgttcttgttctctg---cagaaaagcaaaataaagcctgttcatgttgttgatgttcctggtcatgcagGGCTCAAACCCAAGCTTGATGAAGTCCTGCCTCAAGCAGCTGGGATAGTTTTTGCTGTTGATGCTCAAGATTTCTTGTCCACCATGCAAGTCGTTGCAGA
| ||| | | | ||| | | || || || | ||| | | | || ||| |||| || || | | | || |||| ||| || |||||| | ||||| |||||||||||| |||||||||||||||| || | |||| ||||||||| || ||| || |||| |||||||||| || || |
-----------------------------gtaaagaatcttactgtgttctgttgtaaacaacacgtgcagttgattgtgatggatggaat--aacatattactaaaccatgtcccgtgcttgctctttgtgacagAAAGGAAAAATCAAGCCTGTTCATCTTGTTGATGTTCCTGGGCACTCTCGGCTTCGACCCAAGCTAGAAGAATTCTTGCCCCAAGCAGCTGCCATTGTGT-------------------------------------------------
upper sequence: LOC_Os06g27870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv01s0127g00270.t01 (Vitis vinifera), 3'ss of exon 4
gtaagacgactcattacagagaaatattttcagcgaaaggaagactatctggttat-gtagaaacatgtatttgctgactaaagtgcaattgaacagatggcttgatctctgttcttgttctctgcagaaaagcaaaataaagcctgttcatgttgttgatgttcctggtcatgcagGGCTCAAACCCAAGCTTGATGAAGTCCTGCCTCAAGCAGCTGGGATAGTTTTTGCTGTTGATGCTCAAGATTTCTTGTCCACCATGCAAGTCGTTGCAGA
||| | || |||||| | |||||| | | || | | ||| ||| | || |||||| || ||| | ||| | |||| ||||| | ||||||||||||||||||||||||||||||||||| ||| | | || |||||| || ||||| || ||||||| ||||||||||||||||
-------------gtactt-gcaacattttcctctc------ttctatcttaatgttgtttatatatggattgttaaatacaaacttgattgaagtgagtgctc--tttctatccttg------acagAAGGGTAAAATAAAGCCTGTTCATGTTGTTGATGTTCCTGGGCATTCTCGTCTTCGACCCAAACTGGATGAGTTCTTGCCTCAGGCAGCTGGGATAGTTT------------------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgcagaaaagcaaaataaagcctgttcatgttgttgatgttcctggtcatgcagGGCTCAAACCCAAGCTTGATGAAGTCCTGCCTCAAGCAGCTGGGATAGTTTTTGCTGTTGATGCTCAAGATTTCTTGTCCACCATGCAAGTCGTTGCAGA
tgttgat putative branch site (score: 4)
aaaagcaaaataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagacgactcattacagagaaatattttcagcgaaaggaagactatctggttatgtagaaacatgtatttgctgactaaagtgcaattgaacagatggcttgatctctgttcttgttctctgcagaaaagcaaaataaagcctgttcatgttgttgatgttcctggtcatgcagGGCTCAAACCCAAGCTTGATGAAGTCCTGCCTCAAGCAGCTGGGATAGTTTTTGCTGTTGATGCTCAAGATTTCTTGTCCACCATGCAAGTCGTTGCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT