Sequence
atgc intronic sequence ATGC exonic sequencegttccattcagaattctgcaatttcatctcatttaagatttagagtgacttttccagttttccttcgtcgcaggcttgcatgtacataactattgcatgcttttgttttccgtttgatcaaagttcgtttctgttgtttgtagGTTAATCCTGCTTCTGCTGGGGCTCAGTATGACAGAGAATTTATTGTTTGTTCTCTTGATTTGCTTTCTGGACTTGCTGAAGGGCTTGGCAGTGGGATAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G16950.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G16950.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA10G42960.1 (Glycine max), 3'ss of exon 19
gttccattcagaattctg--caatttcatctcatttaagatttagagtgacttttccagttttccttcgtcgcaggcttgcatgtacataactattgcatgcttttgttttccgtttgatcaaagttcgtttctgttgtttgtagGTTAATCCTGCTTCTGCT---GGGGCTCAGTATGACAGAGAATTTATTGTTTGTTCTCTTGATTTGCTTTCTGGACTTGCTGAAGGGCTTGGCAGTGGGATAG
||||| | ||| | ||||| ||||| | | | || || | ||| || | || ||| | |||| |||| || | ||| | || || | || ||| | ||||||| | | |||| ||||||||||| || |||||||| || ||||||||||||||||||||||| || || || |||||||||||||
------------gttctggttacttttgcattatttatgatttgtctagcagactactgtattaccacgtaccaaaagggtctg---------attttgaggttttattttatcttccaacaagttgagtgtcattctatttcagGCTGATCCTGCCGCCACCACAGGGGTTCAGTATGACAAGGAGTTTATTGTATGCTCTCTTGATTTGCTTTCTGGACTAGCAGAGGGTCTTGGCAGTGGGA---
upper sequence: AT2G16950.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA20G24040.1 (Glycine max), 3'ss of exon 19
gttccattcagaattctgcaatttcatctcatttaagatttagagtgacttttccagttttccttcgtcgcaggcttgcatgtacataactattgcatgcttttgttttccgtttgatcaaagttcgtttctgttgtttgtagGTTAATCCTGCTTCTGCT---GGGGCTCAGTATGACAGAGAATTTATTGTTTGTTCTCTTGATTTGCTTTCTGGACTTGCTGAAGGGCTTGGCAGTGGGATAG
| || |||| | || || | | | || ||| | || || | |||| |||| || | ||| | || || | || ||| | ||||||| | | |||| ||||||||||| || |||||||| || ||||||||||||||||||||||| || || || ||||||||||| |
-------------------------------------gtctaaca-gactact---gtattaccgctttcca--cttaccaataggggctgtttttgagattttattttatcttccaacaagttgagtgtcattctatttcagGCTGATCCTGCCGCCACCACAGGGGTTCAGTATGACAAGGAGTTTATTGTATGCTCTCTTGATTTGCTTTCTGGACTAGCAGAGGGTCTTGGCAGTGGAA---
upper sequence: AT2G16950.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv03s0038g02830.t01 (Vitis vinifera), 3'ss of exon 19
gttccattcagaattctgcaatttcatctcatttaagatttagagtgacttttccagttttccttcgtcgcaggcttgcatgtacataactattgcatgcttttgttttccgtttgatcaaagttcgtttctgttgtttgtagGTTAATCCTGCTTCTGCTGGGGCTCAGTATGACAGAGAATTTATTGTTTGTTCTCTTGATTTGCTTTCTGGACTTGCTGAAGGGCTTGGCAGTGGGATAG
|||| | | | | | || | | | | | || | || || | || || || | ||| || || |||| ||| || || |||||||||| ||||| | ||||||||| | ||| |||||||| || ||||| || ||||| ||||||||||| ||||| ||||| ||||||||||
------------------------------------tgcttagctggtcgcattatatgtagctcctttaaaagtt--aatttgaatgacaagaatatagtt---gttacaacttg--cagtttttgttttgacacttttcagATTGATCCTGCTTCAGCTGGTGTTCAGTATGATAAAGAGTTTATTGTATGCTCTCTCGACTTGCTGTCTGGACTTGCAGAAGGTCTTGGTAGTGGGATAG
upper sequence: AT2G16950.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: PP1S276_77V6.1 (Physcomitrella patens), 3'ss of exon 19
gttccattcagaattctgcaatttcatctcatttaagatttagagtgacttttccagttttccttcgtcgcaggcttgcatgtac-ataactattgcatgcttttgttttccgtttgatcaaagt-tcgtttctgttgtt-tgtagGTTAATCCTGCTTCTGCTGGGGCTCAGTATGACAGAGAATTTATTGTTTGTTCTCTTGATTTGCTTTCTGGACTTGCTGAAGGGCTTGGCAGTGGGATAG
| | || || || | | || | | ||| | | |||| | || | | | || | | || | || | |||||| | ||| || || | | || |||| ||||||||| ||||||||| | |||||||| || |||||||||||||| ||||| || | || |
----------------------------------------------gcttattacaacttactagagctttttactggtacgtattgttagcattgtgagattcataatgaactgcgtctaatgcattgtccccattttggtgtagGCCGACCCTCAGAGCGCAGGCGTGAATTACGACAAAGAATTTATAGTTTGTTCTTTAGATTTGCTCTCGGGACTTGCTGAAGGCCTTGGGAGCAGTATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actattgcatgcttttgttttccgtttgatcaaagttcgtttctgttgtttgtagGTTAATCCTGCTTCTGCTGGGGCTCAGTATGACAGAGAATTTATTGTTTGTTCTCTTGATTTGCTTTCTGGACTTGCTGAAGGGCTTGGCAGTGGGATAG
tttctgtt CT-rich tract
ttttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttccattcagaattctgcaatttcatctcatttaagatttagagtgacttttccagttttccttcgtcgcaggcttgcatgtacataactattgcatgcttttgttttccgtttgatcaaagttcgtttctgttgtttgtagGTTAATCCTGCTTCTGCTGGGGCTCAGTATGACAGAGAATTTATTGTTTGTTCTCTTGATTTGCTTTCTGGACTTGCTGAAGGGCTTGGCAGTGGGATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG