Sequence
atgc intronic sequence ATGC exonic sequencegtgtgttttttatttttgattacctaatacctacacatatttttgctattcgtgctcaatatcatcttctttataatgtagCCTGGTGATTTGGAAAAAGCTCAACTTGGACTAGCTCATAGCTACAGCAGAGCAAAGGTGAAGTTCAATGTTAACCGGGTGGATAACATGGTTATTCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G12860.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G12860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g46720.2 (Oryza sativa), 3'ss of exon 2
------------------gtgtgttttttatttttgattacctaatacc-tacacatatttttgctattcgtgctcaatatcatcttctttataatgtagCCTGGTGATTTGGAAAAAGCTCAACTTGGACTAGCTCATAGCTACAGCAGAGCAAAGGTGAAGTTCAATGTTAACCGGGTGGATAACATGGTTATTCAAG
|| ||| | || || | ||| | | | | || | || || | || | | ||| | || |||| ||| |||||||| ||||| || || || | |||||||| ||||| |||||||| ||||||||||| ||||| |||||||||||||| |||||||
tgttggactgcaatgctttgatgctttcatatgttccttgcataaaatggtttttttcctgttattgtttgtttacttgctcctttgttttcgattgcagCCAACTGACTTGGAAAAGGCTCAGCTAGGCCTGGGGCATAGCTATAGCAGGGCAAAGGTTAAGTTCAATGTGAACCGTGTGGATAACATGGTAATTCAAG
upper sequence: AT3G12860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g22880.1 (Oryza sativa), 3'ss of exon 2
----------------gtgtgtttttta-tttttgattacctaatacctacacatatttttgctattcgtgctcaatatcatcttcttta---taatgtagCCTGGTGATTTGGAAAAAGCTCAACTTGGACTAGCTCATAGCTACAGCAGAGCAAAGGTGAAGTTCAATGTTAACCGGGTGGATAACATGGTTATTCAAG
||||| || | || || | ||| | | ||| | | | |||| | | | | || | | || | ||| || ||||| || || || ||||| || | ||||||||||||||| || ||||||||||||||||| ||||| || || |||||||| ||||| |
caaagaaaaatcttgtatgtgtgcttaagttcaaaatctcgtaaagaaaaaatgtatgtacacccgtt-tgcttattctggttttgtgtgatttactttagAAATCGGACTTGGAGAAGGCGCAGCTTGGCCTGGGTCATAGCTACAGCAGGGCGAAGGTGAAGTTCAATGTGAACCGCGTTGACAACATGGTGATTCAGG
upper sequence: AT3G12860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G110233_T01 (Zea mays), 3'ss of exon 2
---------------gtgtgttttttat-ttttgattacctaatacctacacatatttt-tgct--attcgtgctcaatatcatcttctttataatgtagCCTGGTGATTTGGAAAAAGCTCAACTTGGACTAGCTCATAGCTACAGCAGAGCAAAGGTGAAGTTCAATGTTAACCGGGTGGATAACATGGTTATTCAAG
|| |||| ||| | ||| | | ||| || | | |||| ||| | | | || | | | ||||| | ||| ||||| || || |||||||| || | |||||||||||||| || ||||||||||||||||| || || || ||||||||||| || ||||
tgatgagcttacgcattgctttttatatgcctaaattgttgtaaagctaaacgcctgctgtgcttaatttggctttaccatgtgtccatgttgattgtagGATTCTGACTTGGAGAAGGCCCAACTTGGCCTGGGGCATAGCTACAGCAGGGCTAAGGTGAAGTTCAATGTGAATCGTGTTGATAACATGGTGATCCAAG
upper sequence: AT3G12860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G144995_T01 (Zea mays), 3'ss of exon 2
-------------gtgtgttttttatttttgat-tacctaatacctacacatatttt--tgctattcgtgctcaatatcatcttct--ttataat-gtagCCTGGTGATTTGGAAAAAGCTCAACTTGGACTAGCTCATAGCTACAGCAGAGCAAAGGTGAAGTTCAATGTTAACCGGGTGGATAACATGGTTATTCAAG
|| |||| | | || | ||| | || |||| ||||| ||| | | ||| | | || |||| | ||| ||||| || || || ||||| || | |||||||||||||| || ||||||||||||||||| || || || || |||||||| || || |
tgcaaaattttggctgctgggcttatgcatagtgtatcaaattttgttgtgaagttggatgcttgatgtgcttaatttgtttttccgatggtgattgtagGATTCTGACTTGGAGAAGGCCCAGCTTGGCCTGGGGCATAGCTACAGCAGGGCCAAGGTGAAGTTCAATGTGAATCGTGTTGACAACATGGTGATCCAGG
upper sequence: AT3G12860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G13770.1 (Glycine max), 3'ss of exon 2
----------------gtgtgttttt-tatttttgattacctaatacctaca-catatttttgctattcgtgctcaatatcatcttctttataatgt-----------agCCTGGTGATTTGGAAAAAGCTCAACTTGGACTAGCTCATAGCTACAGCAGAGCAAAGGTGAAGTTCAATGTTAACCGGGTGGATAACATGGTTATTCAAG
| | ||||| | ||| || | | ||| || | ||||||| | | | | |||| || || ||||| || || |||| ||||| ||||| || |||||||| || | ||||| ||||||||||||||||||||||| ||||||||||| || || ||||||||||||||||
gttagtgtttcctcatgcctctttttgtgtttctgtgtgcaggataactgtgtcctatttttatcactaat-ttatatat-atattttttatgctgcttgattttcacagTCTGGAGATTTAGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGAGCAAAGGTGAAGTTTAATGTTAACCGTGTTGACAACATGGTTATTCAAG
upper sequence: AT3G12860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G03150.1 (Glycine max), 3'ss of exon 2
------------------------gtgtgttttttatttttgattacctaatacctacacatatttttgctattcgtgctcaatatcatcttctttataat--gtagCCTGGTGATTTGGAAAAAGCTCAACTTGGACTAGCTCATAGCTACAGCAGAGCAAAGGTGAAGTTCAATGTTAACCGGGTGGATAACATGGTTATTCAAG
||||||| | | | |||| | || |||| | | | | | | | || ||| || | || |||| ||||||||||| || |||||||| || | ||||| |||||||| |||||||||||||| ||||||||||| || || ||||||||||||||||
gttagtgtttcctcatgcctccttttgtgtttctgtatccaggacacctgtatcttatttatatcactaatttatatattgtttttgtgctgcttgatttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGGGCAAAGGTGAAGTTTAATGTTAACCGTGTAGACAACATGGTTATTCAAG
upper sequence: AT3G12860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 2
---------------------gtgtgtttttt---atttttgattacc-taatacctacacatat-ttttgctattcgtgct--caatatcatcttcttt----------ataatgtagCCTGGTGATTTGGAAAAAGCTCAACTTGGACTAGCTCATAGCTACAGCAGAGCAAAGGTGAAGTTCAATGTTAACCGGGTGGATAACATGGTTATTCAAG
|||||||||| | || ||| | | || |||| ||| || | | | | | || || || ||| || ||||| | || ||||||||||| || |||||||| || | ||||| |||||||||||||||||||| |||||||||||||| || || |||||||| |||||||
gttagcatttactcctgcctcgtgtgtttttgcagaagcagaatcaccgtgttgtataggaatatatttcgcaagttattttatttaaattattttttttccttgattgaattctgtagTCCGGGGATTTGGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGAGCAAAGGTGAAATTCAATGTTAACCGTGTTGACAACATGGTCATTCAAG
upper sequence: AT3G12860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------gtgtgttttt-tatttttgattacctaatacctacaca-tatttttgctattcgtgctca-atatcatcttctttataatgtagCCTGGTGATTTGGAAAAAGCTCAACTTGGACTAGCTCATAGCTACAGCAGAGCAAAGGTGAAGTTCAATGTTAACCGGGTGGATAACATGGTTATTCAAG
|| ||||| | | || | | ||| || | |||||| | | ||| ||| || | ||| |||||||||| || | ||||| || |||||||| || | || || ||||||||||||||||||||||||||||| ||| | || ||||| ||||| ||||| |
gtttgctttatttattttttccctcaaaatatgcttctgcctttttgtgtattacaacaattaaagggtaggcggtattttctttgcaatttctcttatagtatttatttttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGAGCAAAGGTGAAGTTCAATGTGAACAGAGTCGATAATATGGTCATTCAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacctacacatatttttgctattcgtgctcaatatcatcttctttataatgtagCCTGGTGATTTGGAAAAAGCTCAACTTGGACTAGCTCATAGCTACAGCAGAGCAAAGGTGAAGTTCAATGTTAACCGGGTGGATAACATGGTTATTCAAG
acctaat putative branch site (score: 3)
tcatcttcttt putative PPT
atatttttgctatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgttttttatttttgattacctaatacctacacatatttttgctattcgtgctcaatatcatcttctttataatgtagCCTGGTGATTTGGAAAAAGCTCAACTTGGACTAGCTCATAGCTACAGCAGAGCAAAGGTGAAGTTCAATGTTAACCGGGTGGATAACATGGTTATTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA