Sequence
atgc intronic sequence ATGC exonic sequencegcaagaaatttctcgtatctttactataattctgtttccttgcaatgctgtacttggattttccatcgcaaaatagatgtttacacatctttctgtttcaaagattttcgtcttctactttctaattgttaaactaatttgcactattggtggcatgtggtttcagAATGAGGACGGAGGTTGGGGTTTACATATTGAGGGCCCTAGCACCATGTTTGGGTCTGTGTTGAACTATGTTACTCTAAGGTTGCTTGGAGAAGGACCTA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G07050.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 3
gcaagaaatttctcgtatctttactataattctgtttccttgcaatgctgtacttggattttccatcgcaaaatagatgtttacacatctttctgtttcaaagattttcgtcttctactttctaattgttaaactaatttgcactattggtggcatgtggtttcagAATGAGGACGGAGGTTGGGGTTTACATATTGAGGGCCCTAGCACCATGTTTGGGTCTGTGTTGAACTATGTTACTCTAAGGTTGCTTGGAGAAGGACCTA
| | | | | ||| | | || ||| |||| | | || | ||| | ||||||| || ||||| |||||||| || |||||||||| |||||||||||||| || | ||||| |||||| || | || |||||||| || || ||
------------------------------------------------------------------------------------------gtaagaaatctaattacacttctacaatcttgaaataagtaaaggcaatgttttccttttctgtgtgtaagtgtagAATGAAGATGGAGGATGGGGTTTGCACATTGAGGGCCACAGCACCATGTTTGGCTCAGCGTTGACATATGTTTCTTTGAGATTGCTTGGGGAGGGGCCAG
upper sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G00430.1 (Glycine max), 3'ss of exon 4
gcaagaaatttctcgtatctttactataattctgtttccttgcaatgctgtacttggattttccatcgcaaaatagatgtttacacatctttctgtttcaaagattttcgtcttctactttctaattgttaaactaatttgcactattggtggcatgtggtttcagAATGAGGACGGAGGTTGGGGTTTACATATTGAGGGCCCTAGCACCATGTTTGGGTCTGTGTTGAACTATGTTACTCTAAGGTTGCTTGGAGAAGGACCTA
|| || || | || || | | | | | | ||||| || | || | | ||| || || | | ||||| |||| || || |||||||| |||||||| || || |||||||||||||| ||||| |||| ||| ||||||| || ||||| || || || ||||
------------------------------------------------------------------------gtaagaactt-catgccattttgctccttaatctatgggcttctcct-------------agtagtcctcctaattagttaaatttaactgcagAACAAGGATGGTGGGTGGGGTTTGCATATTGAAGGTCCAAGCACCATGTTTGGCTCTGTCTTGAGTTATATTACTCTGAGATTGCTAGGTGAGGGGCCTA
upper sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 4
gcaagaaatttctcgtatctttactataattctgtttccttgcaatgctgtacttggattttccatcgcaaaatagatgtttacacat--ctttctgttt--caaagattttcgtcttctactttctaattgttaaactaatttgcactat-----tggtggcatgtggtttcagAATGAGGACGGAGGTTGGGGTTTACATATTGAGGGCCCTAGCACCATGTTTGGGTCTGTGTTGAACTATGTTACTCTAAGGTTGCTTGGAGAAGGACCTA
|||| || | || | || || || | || | | | ||| || ||| | ||| ||| |||||| | | | || | | | ||| || | | | | | || ||||| | || || || |||||||||||||| |||||||| |||||||||||||| |||| ||||||||||| ||| ||||||||||||| |||||| |||
-------------------------gtaat-ctacaactatgagaaatcaatctataatcctcttttgccatgtgctttttttttaattacttattatttgttaaaaattttctttatgtgattcttgcctctggggctagcaaacattttaatcataaagatgcataattgcagAACAAAGATGGTGGGTGGGGTTTACATATCGAGGGCCCAAGCACCATGTTTGGTACTGTCTTGAACTATGTAACTTTAAGGTTGCTTGGTGAAGGAGCTAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|47831404|gb|CK121088.1|CK121088EST: TGTCGGAACAACATAAACAAGAAATGCGCCGTTATCTCTATAATCACCAG AATGAGGACGGAGGTTGGGGTTTACATATTGAGGGCCCTAGCACCATGTTT
genomic: TGTCGGAACAACATAAACAAGAAATGCGCCGTTATCTCTATAATCACCAGgcaagaaatt ... gtggtttcagAATGAGGACGGAGGTTGGGGTTTACATATTGAGGGCCCTAGCACCATGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttctactttctaattgttaaactaatttgcactattggtggcatgtggtttcagAATGAGGACGGAGGTTGGGGTTTACATATTGAGGGCCCTAGCACCATGTTTGGGTCTGTGTTGAACTATGTTACTCTAAGGTTGCTTGGAGAAGGACCTA
aactaat putative branch site (score: 2)
tttctaattgttaaac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagaaatttctcgtatctttactataattctgtttccttgcaatgctgtacttggattttccatcgcaaaatagatgtttacacatctttctgtttcaaagattttcgtcttctactttctaattgttaaactaatttgcactattggtggcatgtggtttcagAATGAGGACGGAGGTTGGGGTTTACATATTGAGGGCCCTAGCACCATGTTTGGGTCTGTGTTGAACTATGTTACTCTAAGGTTGCTTGGAGAAGGACCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA