Sequence
atgc intronic sequence ATGC exonic sequencegttttgtgtggctgtatattcttgttttgcaaataatttctttatttatgttttcatgtgtgaaactcttatgcagTACTCAAAGTTTGTGAAGCCAGCATTTGAGGATTTCATACTCCCAACAAAGAAATACGCAGATATAATAATTCCCCGAGGTGGTGATAACCATGTTGCTA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55810.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 3'ss of exon 7
------------------------------------------gttttgtgtggctgtatattcttgtt-ttgcaaataatttctttatttatgttttcatgtg-tgaaactctta---------------tgcagTACTCAAAGTTTGTGAAGCCAGCATTTGAGGATTTCATACTCCCAACAAAGAAATACGCAGATATAATAATTCCCCGAGGTGGTGATAACCATGTTGCTA
||| || | | || | ||| || || || || | || ||| || | || | |||| | ||||||||||||||||| ||||| || ||||| || ||||| |||||||| ||||| || || ||||| || || || |||||||| ||||| ||||||| |
gttacatggtcacatacctttttactcactagagctgtttttatttaacatgtttacaaatcttagttgttaggtcagatctccttgatgattcttttttgaaattaaccacttaattctacttatgttttacagTACTCAAAGTTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACCAAGAAGTATGCTGATATTATCATCCCACGAGGTGGCGATAATGATGTTGCAA
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 7
---------------------------------------------------------------------------gttttgtgtggct--gtatattcttgttttgcaaataatttctttatttatgttttcatgtgtgaaactcttatgcagTACTCAAAGTTTGTGAAGCCAGCATTTGAGGATTTCATACTCCCAACAAAGAAATACGCAGATATAATAATTCCCCGAGGTGGTGATAACCATGTTGCTA
||| | | | | ||| | ||| || | | |||| | | ||| || | | || || | ||||| ||||||||||| ||||| || ||||| || ||||| |||||||| ||||| || || ||||| || || || |||||||| ||||| ||||||| |
gtaacatggtcacatctattactgtttttgtttttcactagttctgtttttatttaacatgtttacaaaatattagttgttacttgttaggtacagacttccttgatgattcatttttgaaattaaccatttaatgctattccttttttacagTATTCAAAGTTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACCAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGATAATGATGTTGCGA
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
-------------------------------------------------------------------------------------------------------gttttgtgtggctgtatattc--ttgttttgcaaataatttctttatttatgttttcatgtgtgaaactcttat--gcagTACTCAAAGTTTGTGAAGCCAGCATTTGAGGATTTCATACTCCCAACAAAGAAATACGCAGATATAATAATTCCCCGAGGTGGTGATAACCATGTTGCTA
| ||| | | |||| ||| | | | || | | | | || |||| | |||| ||| | ||||||||||| ||||| ||||| || ||||| || ||||| |||||||| ||||| || || ||||| || || || |||||||| || || |||| || |
gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatag-tgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 7
------------------gttttgtgtggctgtatattcttgtt--ttgcaaataatttctttatttatgtt-----ttcatgtgtgaaactcttatgcagTACTCAAAGTTTGTGAAGCCAGCATTTGAGGATTTCATACTCCCAACAAAGAAATACGCAGATATAATAATTCCCCGAGGTGGTGATAACCATGTTGCTA
|||| | | | | | | | ||| | | | | || | |||| |||| ||| | ||| | ||| | ||||||| ||||| |||||||||||||| ||||| || || || || ||||||||||| || || |||||||| || ||||| || || ||||| ||||| || |
aattttaatcaagctatcattttctttatcagattttgatggttaatatctaccatttaatggatttgtgttgctgattcttatgtaatacttgt-tgcagTATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCA
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 7
-----------------------gttttgtgtggctgtatattcttgttttgcaaataatttctttatttatgtt-ttcatgtgtgaaactcttatgcagTACTCAAAGTTTGTGAAGCCAGCATTTGAGGATTTCATACTCCCAACAAAGAAATACGCAGATATAATAATTCCCCGAGGTGGTGATAACCATGTTGCTA-
||| | | || || | | || ||| ||| | | | ||| | ||| | ||| | ||||||| ||||| |||||||||||||| ||||| || || || || ||||||||||| || || |||||||| || ||||| || || ||||| ||||| || |
aatattaatcaagctatcatattctttatcagagtttgatgttaatagctaccattcaatggatttttgtggctgattcttatgtaatacttgt-tgcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7
--------------------gttttgtgtggctgtatattcttgtt--ttgcaaataatttctttatttatgtt--ttcatgtgtgaaactcttatgcagTACTCAAAGTTTGTGAAGCCAGCATTTGAGGATTTCATACTCCCAACAAAGAAATACGCAGATATAATAATTCCCCGAGGTGGTGATAACCATGTTGCTA
| | || | | || || | | ||| || ||||| | | | | | | | | || | ||||||||||||| |||||||||||||| ||||| || || ||||| ||||||||||| || |||||||| || |||||||| || || || || ||||| || |
tttaacttagaggttaatgcaatcagattgcttttcagtttttatgcatgttgtatacttcctttaatgttaataatccttttatttaatcttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S19_94V6.1 (Physcomitrella patens), 3'ss of exon 6
----------gttttgtgtggctgtatattcttgttttgcaaat---aatttctttatttatg-----ttttcatgtgtgaaactct-------tatgcagTACTCAAAGTTTGTGAAGCCAGCATTTGAGGATTTCATACTCCCAACAAAGAAATACGCAGATATAATAATTCCCCGAGGTGGTGATAACCATGTTGCTA
| |||| || | | |||| | | | | || || | |||| | ||| || ||| || ||||||| ||||||||||||||||||| ||||| ||||| || | ||||||||||| || || ||| | || | ||||| || || || || ||||| ||||
gaccatcccagccttgt-tgtccatggcgtcttagtgcgaacacttcgatctcgtagcttatacggaatgaagatgaactaacttctggaggtgtacgcagTACGCAAAGTTTGTGAAGCCAGCGTTTGATGATTTTATTTTGCCAACAAAGAAGTATGCGGATGTCATCTTACCCCGTGGAGGAGACAATCATGTGGCTA
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S488_8V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------gttttgtgtggctgtatattcttgttttgcaaataattt--ctttatt-tatgttttcatgtgtgaaact----------cttatgcagTACTCAAAGTTTGTGAAGCCAGCATTTGAGGATTTCATACTCCCAACAAAGAAATACGCAGATATAATAATTCCCCGAGGTGGTGATAACCATGTTGCTA
| | ||||| | || | || || || | | || | || || | || | || ||||||| ||||||||||||||||||||||||| ||||| || | ||||||||||| || || ||| | || | ||||| ||||| || || ||||| || |
gccatctgaatcctatccgtggcagcgtaatgagtacttttggatcatgtagcgttgtcgcatattgaagagaaacgaattgtattttggatttgtgcagTATGCAAAGTTTGTGAAGCCAGCATTTGATGATTTTATTTTGCCAACAAAGAAGTATGCGGATGTCATCTTACCCCGTGGTGGAGACAATCATGTGGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttttgcaaataatttctttatttatgttttcatgtgtgaaactcttatgcagTACTCAAAGTTTGTGAAGCCAGCATTTGAGGATTTCATACTCCCAACAAAGAAATACGCAGATATAATAATTCCCCGAGGTGGTGATAACCATGTTGCTA
ctcttat CT-rich tract
aaataatttctttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttgtgtggctgtatattcttgttttgcaaataatttctttatttatgttttcatgtgtgaaactcttatgcagTACTCAAAGTTTGTGAAGCCAGCATTTGAGGATTTCATACTCCCAACAAAGAAATACGCAGATATAATAATTCCCCGAGGTGGTGATAACCATGTTGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT