Sequence
atgc intronic sequence ATGC exonic sequencegtaagattgatcacaaattctttattaaactactagatatgataaggatgaactagtttgcttgtatacaaaggttagaaggtattacttattgccatatattaataacatctgagaagtacctaagcctctattttgttggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGAAAGCTGACTGATAGATCAGATGTTTTCTCGTTTGGGGTTGTTCTCTTAGAGCTTATAACAGGACGCAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G70460.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G70460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G39480.1 (Glycine max), 3'ss of exon 7
gtaagattgatcacaaattctttattaaactactagatatgataaggatgaactagtttgcttgtatacaaaggttagaaggtattacttattgccatatattaataacatctga-gaagtacctaagcctctattttgttggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGAAAGCTGACTGATAGATCAGATGTTTTCTCGTTTGGGGTTGTTCTCTTAGAGCTTATAACAGGACGCAAA
|| ||| ||||| | | || | | || | || | ||| || ||||| || | || | ||| || || || |||| || |||||||| |||| |||||||||||| ||||||||| | || |||||||||||||||||||| ||||||||||| ||| | |||||| |||| ||| | |||
-------------------------------------------aaacatg---tagttcaataatgtagatacatttgctggaaaaccttctt---------caataatgtccaataaaattactacaccaactcgtttctgactttaatt-tcagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACGGATAGATCAGATGTTTTCTCATTTGGGGTTGTCCTCCTTGAGCTTGTAACTGGAAGGAAA
upper sequence: AT1G70460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G03690.1 (Glycine max), 3'ss of exon 6
gtaagattgatcacaaattctttattaaactactagatatgataaggatgaactagtttgcttgta-tacaaaggttagaaggtattacttattgccatatattaataacatctgagaagtacctaagcctctattttgttggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGAAAGCTGACTGATAGATCAGATGTTTTCTCGTTTGGGGTTGTTCTCTTAGAGCTTATAACAGGACGCAAA
| | || || | ||| ||| ||| | || | | || ||| | | || |||| | || || | |||| || ||||||| |||| |||||||||||| ||||||||| | || |||||||||||||||||||| ||||| ||||| ||| | ||||||||||| ||| | |||
----------------------------------------------------ttttgaagtttataatggaaactttatcagggaaaaccttcagtaatgc-caaatgctaaacta-aactaccacacttactcattc--tagcttcatttcgcagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACAGATAGATCAGATGTTTTCTCTTTTGGAGTTGTCCTCCTTGAGCTTATAACTGGAAGGAAA
upper sequence: AT1G70460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G19100.1 (Glycine max), 3'ss of exon 5
gtaagattgatcacaaattctttattaaactactagatatgataaggatgaactagtttgcttgtatacaaaggttagaaggtattacttattgccatatattaataacatctga--gaagtacctaagcctctattttgttggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGAAAGCTGACTGATAGATCAGATGTTTTCTCGTTTGGGGTTGTTCTCTTAGAGCTTATAACAGGACGCAAA
|| || ||| | | || | || | || | | | | | ||||| | | || ||| || || ||| |||||| ||| ||||||| |||| |||||||||||| ||||||||| | || || ||||||||||||||||| ||||||||||| ||| | |||||| |||| ||| | |||
--------------------------------------------------aaatattttaataatgtagatgcatttgccgg-----ccggaaaacctttttcaataatgcccaattaaattactacagaaactcattt-ctggcttcaatta-cagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACAGACAGATCAGATGTTTTCTCATTTGGGGTTGTCCTCCTTGAGCTTGTAACGGGAAGGAAA
upper sequence: AT1G70460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G04010.1 (Glycine max), 3'ss of exon 6
gtaagattgatcacaaattctttattaaactactagatatgataaggatgaactagtttgcttgtatacaaaggttagaaggtattacttattgccatatattaataacatctgagaagtacctaagcctctattttgttggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGAAAGCTGACTGATAGATCAGATGTTTTCTCGTTTGGGGTTGTTCTCTTAGAGCTTATAACAGGACGCAAA
| ||||| || ||| ||| | | || | | || ||| | | || || | | || || | |||| || ||||||| |||| ||||| |||||| ||||||||| | || |||||||||||||||||||| ||||| ||||| || | ||||||||||| ||| | |||
-------------------------------------------------gtttgagtttata---atggaaacattatcaaagaaaaccttcagtaatgc-caaatgctaaactaaaactatcatactaactcattc--tagcttcatttcgcagGTACATGGCTCCAGAGTATGCAACAAGTGGAAAATTAACAGATAGATCAGATGTTTTCTCTTTTGGAGTTGTCCTTCTTGAGCTTATAACTGGAAGGAAA
upper sequence: AT1G70460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0127g00670.t01 (Vitis vinifera), 3'ss of exon 5
gtaagattgatcacaaattctttattaaactactagatatgataaggatgaactagtttgcttgtatacaaaggttagaaggtattacttattgccatatattaataacatctgagaagtacctaagcctctattttgttggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGAAAGCTGACTGATAGATCAGATGTTTTCTCGTTTGGGGTTGTTCTCTTAGAGCTTATAACAGGACGCAAA
|||||| | || | | ||| || | | | | || | || || || |||| | | | | ||| | || ||| | | |||||||| |||||||||| |||||| |||||| || ||||||||||||| ||||| ||||| || ||||| || || ||||||||||||||||| || |||
----------------------------------------aataagggaaagtaagaaagagc---tgcaa---ttcaagatttccaactgttctcctaaatgcatc---tctggtgattgtcata----ctaat--gtccagtttggctttcagGTACATGGCACCAGAGTATGCATCAAGTGGGAAATTGACTGATAGATCTGATGTATTCTCATTCGGGGTGGTACTTTTAGAGCTTATAACAGGGCGTAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaataacatctgagaagtacctaagcctctattttgttggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGAAAGCTGACTGATAGATCAGATGTTTTCTCGTTTGGGGTTGTTCTCTTAGAGCTTATAACAGGACGCAAA
taataac putative branch site (score: 1)
cttttgtt putative PPT
tattttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagattgatcacaaattctttattaaactactagatatgataaggatgaactagtttgcttgtatacaaaggttagaaggtattacttattgccatatattaataacatctgagaagtacctaagcctctattttgttggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGAAAGCTGACTGATAGATCAGATGTTTTCTCGTTTGGGGTTGTTCTCTTAGAGCTTATAACAGGACGCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT