Sequence
atgc intronic sequence ATGC exonic sequencegtatatgaaagaaactttcattgcctcttctatgaatagtgattacaaggaatttacttaattgttatactcaaatctctagGGTGCTATTATGGCTGTTGGAGCGTCAAAGCCAACTGTAGTTGCTGATAAGGATGGATTCTTCAGTGTAAAAAACACAATGCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G25860.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G25860.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G121200_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------------------------------------------gtatatgaaagaaactttcattgcctcttctatgaatagtgattacaaggaatttacttaattg--------ttatactcaaatctctagGGTGCTATTATGGCTGTTGGAGCGTCAAAGCCAACTGTAGTTGCTGATAAGGATGGATTCTTCAGTGTAAAAAACACAATGCTG
|| | ||| | | | | | | |||| ||| | |||| |||| || | || | |||| ||||| ||||||||||||||||||| || |||||||| |||||||||||||| ||||| ||| | || | |||||||
gtgggtttcttccctggtgtatgttgtctgtccagttagtatgaaatgttgatagaattgtatgggtttcttccctggtgtctgatgtttgtctagttagtatgaaatgttgatag-aattgtattctattttattaaacacaagaagattgcatggttatatgcagGGGGCTATCATGGCTGTTGGAGCGTCAAGACCTACTGTAGTGGCTGATAAGGATGGTTTCTTTAGTATCAAGAGTGAAATGCTG
upper sequence: AT3G25860.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G24830.1 (Glycine max), 3'ss of exon 3
-------------------------gtatatgaaagaaactttcattgcctcttctatgaatagtgattacaaggaatttacttaattgttatactcaa------atctctagGGTGCTATTATGGCTGTTGGAGCGTCAAAGCCAACTGTAGTTGCTGATAAGGATGGATTCTTCAGTGTAAAAAACACAATGCTG
| | | | ||| || | || | | ||| || | |||| | ||| ||| || || |||||||||| ||||||||||| || |||||||| ||||| | |||||||| |||||||||||||| || || || | |||||||
gttagtgatgatttctgggactttgaagtcttgatttgagagatgttgtggctcat-tgtgtggcaatttgaacgt-tttatctgggggttcaactttgccctttatttccagGGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG
upper sequence: AT3G25860.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0011g03380.t01 (Vitis vinifera), 3'ss of exon 4
-----gtatatgaaagaaactttcattgcctcttctatgaatagtgattacaag-----gaatttacttaattgttatactcaaatct---------ctagGGTGCTATTATGGCTGTTGGAGCGTCAAAGCCAACTGTAGTTGCTGATAAGGATGGATTCTTCAGTGTAAAAAACACAATGCTG
| | ||||||| | | | | | || | | | | || | |||| | |||| ||||| ||||| |||||||| |||||||| ||||| || ||||||| ||||||||||||||||| |||| | |||||||
gtgagttgcaaagccaggactttcacctctattagttcataagattcttctgcccttttgggcatgtgtgagctttttctcaaaatttggaatgatgtcagGGGGCTATCATGGCCGTTGGAGCTTCAAAGCCTACTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGMapped 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|86086933|gb|DR382692.1|DR382692EST: TCGGTATGTTTGGAGTGGATAGATTTGACGCTATTCTTCCGCCAGGACAG GGTGCTATTATGGCTGTTGGAGCGTCAAAGCCAACTGTAGTTGCTGATAAG
genomic: TCGGTATGTTTGGAGTGGATAGATTTGACGCTATTCTTCCGCCAGGACAGgtatatgaaa ... aaatctctagGGTGCTATTATGGCTGTTGGAGCGTCAAAGCCAACTGTAGTTGCTGATAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctatgaatagtgattacaaggaatttacttaattgttatactcaaatctctagGGTGCTATTATGGCTGTTGGAGCGTCAAAGCCAACTGTAGTTGCTGATAAGGATGGATTCTTCAGTGTAAAAAACACAATGCTG
acttaat putative branch site (score: 4)
tctct putative PPT
aatttacttaattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatgaaagaaactttcattgcctcttctatgaatagtgattacaaggaatttacttaattgttatactcaaatctctagGGTGCTATTATGGCTGTTGGAGCGTCAAAGCCAACTGTAGTTGCTGATAAGGATGGATTCTTCAGTGTAAAAAACACAATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG