Sequence
atgc intronic sequence ATGC exonic sequencegtgttttgaacacatatgatacacgtagttttggatttttttatgggaacttctcactcatagtatatctcccaactgactcatgcagATAATGTCAGTACAATCAAAGAGTGATGGGGTCAACACTTCTCTTTTCGAAAAGAGAGAACATATAGAGAAACTGCACCGGACTCGTAATCTTCTTCGTA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G02030.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G02030.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G01610.1 (Glycine max), 3'ss of exon 3
---------gtgttttgaacacatatgatacacgtagttttggatttt--tttatgggaacttctcactcatagtatatctcccaactgactcatgcagATAATGTCAGTACAATCAAAGAGTGATGGGGTCAACACTTCTCTTTTCGAAAAGAGAGAACATATAGAGAAACTGCACCGGACTCGTAATCTTCTTCGTA
| || ||| | || ||| | ||| | | | | ||| | | |||| | || | | | |||||||||||||| || || || | ||||| | |||||||||||||| || || || || || ||||| ||||||||||| |||||| |||||||||||||||
gtaaccgtagcgtactgactatat-tgaaatgattagaatcaaaatgaaaataggatgaaagggactttgataggaattcacatttttctccaatgcagATAATGTCTGTGCAGTCGAGAAGTGACAGTGTCAACACTTCTCTATTTGACAAAAGGGAGCATATTGAGAAACTGCATCGGACTTGTAATCTTCTTCGTA
upper sequence: AT4G02030.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G01660.1 (Glycine max), 3'ss of exon 3
---------gtgttttgaacacatatgatacacgtagttttggatttttttatgg-gaacttctcactcatagtatatctcccaactgactcatgcagATAATGTCAGTACAATCAAAGAGTGATGGGGTCAACACTTCTCTTTTCGAAAAGAGAGAACATATAGAGAAACTGCACCGGACTCGTAATCTTCTTCGTA
|||| | | | || | | | | | || | | ||| |||||| | ||| | | | |||||||||||||| || || || | ||||| | |||||||||||||| || || || || || ||||| |||||||| || |||||| |||||||||||||||
gtaaccgttgtgtacttactatatttaaaatattagaatcaaaatgaaaagaggaagaaagggagtttcatagga-atccgcattttctccaatgcagATAATGTCTGTGCAGTCGAGAAGTGACAGTGTCAACACTTCTCTATTTGACAAAAGGGAGCATATTGAGAAACTACATCGGACTTGTAATCTTCTTCGTA
upper sequence: AT4G02030.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0005g01440.t01 (Vitis vinifera), 3'ss of exon 3
gtgttttgaacacatatgatacacgtagttttggatt-----tttttatgggaacttctcactcatagtatatctcccaactgactcat-gcagATAATGTCAGTACAATCAAAGAGTGATGGGGTCAACACTTCTCTTTTCGAAAAGAGAGAACATATAGAGAAACTGCACCGGACTCGTAATCTTCTTCGTA
||| || || | | | | || | ||||| | ||| || || || || | | || | || |||||||||||| || ||||| | ||||||||||| || || |||||||| || || |||||||||||||||||| |||| || || || ||||||||||| |
gtgcttggataatttttatttcaatcaattttgtgctcactctttcaataaaaagaatgtgaacaagaggtaattggctacacccatattgcagATAATGTCTGTTCAATCTAGAAGTGATGGGGTTAATACCTCTCTTTTTGAGAAAAGAGAACATATAGAGAAATTGCATCGAACACGAAATCTTCTTCGGAMapped 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|19876508|gb|AU237339.1|AU237339EST: AGAGTAATATTTTCGGGATGGAAGGCAATATGGACCAGCTTCTTCAGAAG ATAATGTCAGTACAATCAAAGAGTGATGGGGTCAACACTTCTCTTTTCGAA
genomic: AGAGTAATATTTTCGGGATGGAAGGCAATATGGACCAGCTTCTTCAGAAGgtgttttgaa ... actcatgcagATAATGTCAGTACAATCAAAGAGTGATGGGGTCAACACTTCTCTTTTCGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttttttatgggaacttctcactcatagtatatctcccaactgactcatgcagATAATGTCAGTACAATCAAAGAGTGATGGGGTCAACACTTCTCTTTTCGAAAAGAGAGAACATATAGAGAAACTGCACCGGACTCGTAATCTTCTTCGTA
aactgac putative branch site (score: 2)
atagtatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgttttgaacacatatgatacacgtagttttggatttttttatgggaacttctcactcatagtatatctcccaactgactcatgcagATAATGTCAGTACAATCAAAGAGTGATGGGGTCAACACTTCTCTTTTCGAAAAGAGAGAACATATAGAGAAACTGCACCGGACTCGTAATCTTCTTCGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA