Sequence
atgc intronic sequence ATGC exonic sequencegtatgcttctaatatctcctttgttctttgatcgcttatttatattgattctatatataatgatgttgtatgttgtcacagAACCTTGAAATCAAGAAGATAAATGAAGAAAAGAAGGCTTCCATGGCAGCTCAGTTTGCAGCAGAAGCTTCTCTTCGTAGGGTTCATGCTGCTCAAAAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G14840.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 3'ss of exon 3
gtatgcttctaatatctcctttgttctttgatcgcttatttatatt------gattctatatataatgatgttgtatgttgtcacagAACCTTGAAATCAAGAAGATAAATGAAGAAAAGAAGGCTTCCATGGCAGCTCAGTTTGCAGCAGAAGCTTCTCTTCGTAGGGTTCATGCTGCTCAAAAGG
||||| ||| ||| | | | | | ||| || | | | || ||| | | | ||| ||| | | ||||| || ||| |||||||||| ||||| || || |||||| | ||||| |||||||||||||||||||| || | || || || ||||| || |||||||
gtatgtatcttataatttgtgtttatctgtatccgttgtctctgttttagctgatcttttctttaacaatgataaaaacaaatgcagAATCTAGAAGTCAAGAAGATTAATGATGAGAAAAAGGCTGCAATGGCTGCTCAGTTTGCAGCAGAAGCGACTTTGCGGAGAGTACATGCAGCCCAAAAGG
upper sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 3
gta-tgcttctaatatctcctttgttctttgatcgcttatttatattgattctata------tataatgatgttgtatgttg-tcacagAACCTTGAAATCAAGAAGATAAATGAAGAAAAGAAGGCTTCCATGGCAGCTCAGTTTGCAGCAGAAGCTTCTCTTCGTAGGGTTCATGCTGCTCAAAAGG
||| ||||| | ||| | | || | | || | || | | | | | || || || | ||||| |||||||| ||||| || ||||| |||||||| || || |||||||||||||||||||| ||||| ||||||| ||||| ||||||||||| ||||
gtaatgcttgaagcctctatcaagcttagcgaggagtaaatttctgaggttacgtggtgtgtttttactaaactggatatttcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
upper sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 3
gta-tgcttctaatatctcctttgttctttgatcgcttatttatattgattc-----tatatataatgatgttgtatgttgtcacagAACCTTGAAATCAAGAAGATAAATGAAGAAAAGAAGGCTTCCATGGCAGCTCAGTTTGCAGCAGAAGCTTCTCTTCGTAGGGTTCATGCTGCTCAAAAGG
||| ||||| | ||| | | ||| | | | || | | | || | | | |||| | | | || | ||||| |||||||| ||||| || ||||| ||||| || || || |||||||||||||||||||| ||||| ||||||| ||||| ||||||||||| ||||
gtaatgcttgaagcctctatcaagcttagtgagaggtaaattttttaggttacgtggtgtgtttaataaactgggtatttcttgcagAATCTTGAAATAAAGAAAATCAATGATGAAAAAAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
upper sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 3
gtatgcttctaa-----tatctcctttgttctttgatcgcttatttatatt-gattctatatataatgatgttgtatgttg-tcacagAACCTTGAAATCAAGAAGATAAATGAAGAAAAGAAGGCTTCCATGGCAGCTCAGTTTGCAGCAGAAGCTTCTCTTCGTAGGGTTCATGCTGCTCAAAAGG
|||| | || ||| |||| | | || || | || | | ||| | | ||| || || || | ||||| |||||||| || || || || || ||||||||||| || |||||||||||||||||||| ||||| ||||||| ||||| || ||||| || || |
gtatttcttgaagcctccatcaactttagtaaatagtcattttcccaggttaggtggtatgttttctga-attaaatatttctggcagAATCTTGAAATAAAAAAAATCAACGATGAAAAGAAGGCATCAATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCACGCTGCCCAGAAAG
upper sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 3
-----gtatgcttctaatatctcctttgttctttgatcgcttatttatatt-gattctatatataatgatgttgtatgttg-tcacagAACCTTGAAATCAAGAAGATAAATGAAGAAAAGAAGGCTTCCATGGCAGCTCAGTTTGCAGCAGAAGCTTCTCTTCGTAGGGTTCATGCTGCTCAAAAGG
| ||| | |||| |||| | || || | || | | ||| | | ||| | | || || | ||||| |||||||| || || || || || |||||||| || || |||||||||||||||||||| ||||| ||||| | ||||| |||||||| || || |
gtattgcatgaagcctctatcaactttaggaaatagtcattttcccaggttaggtggtatgttttctga-atcgaatatttctggcagAATCTTGAAATTAAAAAAATCAACGATGAAAAGAAAGCATCAATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTAGAAGGGTCCATGCTGCCCAGAAAG
upper sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 3
gtat-gcttctaatatctcctttgttctttgatcgctt-atttatattgattctata-tataatgatgttgtatgttgtc-acagAACCTTGAAATCAAGAAGATAAATGAAGAAAAGAAGGCTTCCATGGCAGCTCAGTTTGCAGCAGAAGCTTCTCTTCGTAGGGTTCATGCTGCTCAAAAGG
|||| || | || ||| || |||||| | || | | | | || | | | | | | |||| | ||||| || || |||||||| || ||||| ||||||||||| |||||||| ||||| |||||||||||||| ||||| | |||||||||||||| || ||||
gtattgcatgaaacccttccatttttctttataagttttgtgtgtgtgtgttttgcagttttgtcctaacaattgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgatcgcttatttatattgattctatatataatgatgttgtatgttgtcacagAACCTTGAAATCAAGAAGATAAATGAAGAAAAGAAGGCTTCCATGGCAGCTCAGTTTGCAGCAGAAGCTTCTCTTCGTAGGGTTCATGCTGCTCAAAAGG
tattgat putative branch site (score: 3)
ttatttatattgattc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcttctaatatctcctttgttctttgatcgcttatttatattgattctatatataatgatgttgtatgttgtcacagAACCTTGAAATCAAGAAGATAAATGAAGAAAAGAAGGCTTCCATGGCAGCTCAGTTTGCAGCAGAAGCTTCTCTTCGTAGGGTTCATGCTGCTCAAAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT