Sequence
atgc intronic sequence ATGC exonic sequencegtaaacacttactttgtctcttttatctccttaagagcttgtttacttgttgctgttatagagaattgttgtgttgtagctttgtagggcctttgttgttgtcaaactttgcatgtagttgctttactcttttgaggaagaggctcgtgatagtgttttatggattttcgatgaatttgcagATGGATAGAGCATCAATACTTGGAGATGCAATTGATTATCTGAAGGAACTTCTACAAAGGATCAATGATCTTCACAATGAACTTGAGTCAACTCCTCCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G26744.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G26744.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g70310.1 (Oryza sativa), 3'ss of exon 2
gtaaacacttactttgtctcttttatctccttaagagcttgtttacttgttgctgttatagagaattgttgtgttgtagctttgtagggcctttgttgttgtcaaactttgcatgtagttgctttactcttttgaggaagaggctcgtgatagtgttttatggattttcgatgaatttg---cagATGGATAGAGCATCAATACTTGGAGATGCAATTGATTATCTGAAGGAACTTCTACAAAGGATCAATGATCTTCACAATGAACTTGAGTCAACTCCTCCTG
| ||| || || || ||| || || || | | | || | | | | | | | || || | ||||| |||| |||||||| ||||| || || ||||| ||||||||||| || ||||||| || || || ||||| || ||||||||||||||||||||||| |||||
-------------------------------------------------------------------------------ttatgtcaaagtgttcttaatgccaa-ctatgtctg-actcgtttcatgttaatatctata--gtttatcatctcatt--accagttttcttctcctttgtgacagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT
upper sequence: AT3G26744.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G173534_T02 (Zea mays), 3'ss of exon 1
gtaaacacttactttgtctcttttatctccttaagagcttgtttacttgttgctgttatagagaattgttgtgttgtagctttgtagggcctttgttgttgtcaaactttgcatgtagttgctttactcttttgaggaagaggctcgtgatagtgttttatggattttcgatgaatttgcagATGGATAGAGCATCAATACTTGGAGATGCAATTGATTATCTGAAGGAACTTCTACAAAGGATCAATGATCTTCACAATGAACTTGAGTCAACTCCTCCTG
| ||| | | ||| | | | || | | || || | ||| || || || | |||| | | | | || | ||||||||||| || || || ||||| || |||||||| ||||||||||| || || || ||||||| |||||||||||||||||||||||| ||||
---------------------------------------------------------------------------acacgcttggacg--cttcgccatgatagtacat-gtttggtattaatcaacttgctttagtaaatgt----tgattctcatcagcatttctcttctgctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT
upper sequence: AT3G26744.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G05390.1 (Glycine max), 3'ss of exon 1
gtaaacacttactttgtctcttttatctccttaagagcttgtttacttgttgctgttatagagaattgttgtgttgtagctttgtagggcctttgttgttgtcaaactttgcatgtagttgctttactcttttgaggaagaggctcgtgatagtgttttatggattttcgatgaatttgcagATGGATAGAGCATCAATACTTGGAGATGCAATTGATTATCTGAAGGAACTTCTACAAAGGATCAATGATCTTCACAATGAACTTGAGTCAACTCCTCCTG
|||||| || | | | || | | | || | | | || || | ||| | || || || ||| | | || |||| |||||||||| || ||||||||||| ||||||||||| || ||||||| | || || |||| ||||||||||| || || || ||||||||||| ||||
----------------------------------------------------------------------ttgttgttgccattgactggtttattaaggctaagacacttcctttatgtgttgggaactt----aagaatggtgtatggtaatgtcct--------ttcatctgtttgtagATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTGCTGCAGCGGATTAATGATCTTCATAACGAGCTAGAGTCAACTCCACCTG
upper sequence: AT3G26744.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G27480.2 (Glycine max), 3'ss of exon 1
gtaaacacttactttgtctcttttatctccttaagagcttgtttacttgttgctgttatagagaattgttgtgttgtagctttgtagggcctttgttgttgtcaaactttgcatgtagttgctttactcttttgaggaagaggctcgtgatagtgttttatggattttcgatgaatttgcagATGGATAGAGCATCAATACTTGGAGATGCAATTGATTATCTGAAGGAACTTCTACAAAGGATCAATGATCTTCACAATGAACTTGAGTCAACTCCTCCTG
||| | | || ||||| || | | ||| || | | | || | | || || || | |||||||||| || ||||||||||| ||||||||||| || ||||||| | || || |||| ||||||||||| | || || ||||||||||| ||||
-----------------------------------------------------------------------------------------------------------gttg-agacaattcctttatgtattaggagcttagga--atggt-gcatactaatgttctttcatttgttggtagATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTGCTGCAGCGGATTAATGATCTTCATCACGAGCTGGAGTCAACTCCACCTG
upper sequence: AT3G26744.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G27480.1 (Glycine max), 3'ss of exon 1
gtaaacacttactttgtctcttttatctccttaagagcttgtttacttgttgctgttatagagaattgttgtgttgtagctttgtagggcctttgttgttgtcaaactttgcatgtagttgctttactcttttgaggaagaggctcgtgatagtgttttatggattttcgatgaatttgcagATGGATAGAGCATCAATACTTGGAGATGCAATTGATTATCTGAAGGAACTTCTACAAAGGATCAATGATCTTCACAATGAACTTGAGTCAACTCCTCCTG
|||| | | || | || || || || ||| | | || ||||| || | | ||| || | | | || | | || || || | |||||||||| || ||||||||||| ||||||||||| || ||||||| | || || |||| ||||||||||| | || || ||||||||||| ||||
-------------------------------------------------------------------------ttgttgttgc-cagtgactggtttatt----aaggttg-agacaattcctttatgtattaggagcttagga--atggt-gcatactaatgttctttcatttgttggtagATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTGCTGCAGCGGATTAATGATCTTCATCACGAGCTGGAGTCAACTCCACCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttttgaggaagaggctcgtgatagtgttttatggattttcgatgaatttgcagATGGATAGAGCATCAATACTTGGAGATGCAATTGATTATCTGAAGGAACTTCTACAAAGGATCAATGATCTTCACAATGAACTTGAGTCAACTCCTCCTG
tgttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacacttactttgtctcttttatctccttaagagcttgtttacttgttgctgttatagagaattgttgtgttgtagctttgtagggcctttgttgttgtcaaactttgcatgtagttgctttactcttttgaggaagaggctcgtgatagtgttttatggattttcgatgaatttgcagATGGATAGAGCATCAATACTTGGAGATGCAATTGATTATCTGAAGGAACTTCTACAAAGGATCAATGATCTTCACAATGAACTTGAGTCAACTCCTCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC