Sequence
atgc intronic sequence ATGC exonic sequencegttgtttttcttaagcttttgactagtttgaagttttgattactattgattttggactcattcgttcttcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G34660.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G04210.1 (Glycine max), 3'ss of exon 2
--------------------------gttgtttttcttaagcttttgactagtttgaagttttgattacta--ttgattttggactcat-tcgttcttcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG
||||||| || | || | | || | || ||| |||| | | || || | ||||||||||||| ||||| ||||||||||||||||| ||||||||||| ||||| || || || ||||| |||||||
gttacctggttctttgatttcaattctttgttttcatttatagttgatgtcgatttatcccttctcccctaggctgatcatagctccaaatccaattgtgttttcagCATTATCAAAGGGATATTGTTCGTGGTGTAGAAGGTTATATTGTTACTGGATCCAAGCAAGTGGAAATAG
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G01100.2 (Glycine max), 3'ss of exon 2
--------------------------gttgtttttcttaagcttttgactagtttgaagttttgattact--attgattttggactcattcgttcttcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG
| ||||| || |||| || | | | | | | | |||| || | | | ||| ||||||||||| ||||| |||||||| |||||||||||||||||||| || || || || || |||||||||||||
gttacttggtttttctgtacctaccctctatttttgtttgtgttttacctccacttatgctctccctgtttggctgataatgaaatatattgtt------tttcagCATTATCAAAGGGATATTGTCCGTGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAG
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G11950.3 (Glycine max), 3'ss of exon 2
----------------------gttgtttttcttaagcttttgactagtttgaagttttgatta-ctattgattttggactcattcgttcttcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG
|| ||||| || | | | | | | || | | || | | | | | | || | | ||||||||||| ||||| ||||||||||| ||||| ||||||||||| ||||| ||||| || ||||| |||||||
gtgacttggttctttgatttcaattcttttttttcatttatagttcatgtcgatttatcccttctcccctaagctgataatagctccaattgtggtttcagCATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGGTCCAAGCAAGTGGAAATAG
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 2
--------gttgtttttcttaagcttttgactagtttgaagttttgattactattgattttggactcattcgttc--------------ttcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG
||| || | | | | | | | | ||| || ||| | || | || | || |||||||||||| ||||| |||||||| || ||||||||||||||||| || || || || || |||||||||||||
gttaattggtttttctgtaccaaccctctatttttgtttgtgttttatctctacttataccctccctgtttggctgataatgaaatatattgtttttcagCATTATCAAAGGGATATTGTCCGCGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAG
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0001g13530.t01 (Vitis vinifera), 3'ss of exon 2
gttgtttttcttaagcttttgactagtttgaagttttgattactattgattttggac--tcattcgttcttcgttttca---gCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG
|| | || | | ||| | || | | | | |||| || | || | | | ||| | ||| ||||| |||||| |||||||| |||||||||||||||| |||||||| ||||| || |||||||||||||
----gttacacaatgcctcttacttctatgtaactgtcctgtatatttcttcttaacctttgtatatccttttctctcactagCATTTCCAAAGGGATATTGTCCGTGGTGTGGAAGGTTTCATAGTTACTGGGTCCAAGCAAGTTGAAATAG
upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 2
-----gttgtttttcttaagcttttgactagtttgaagttttgattactattgattttggactcattcgttcttcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG
| | | || | | | | | | | || ||| | || | | | | | || |||||||||| ||||| ||||||||||||||||| ||||||| ||| ||||| ||||| ||||||||||||||||
gttgcttaatcctcctgtggttcatttgtgactcaatttgtttatttcctcaacttataaatttctatatcatt---tttcagCATTTTCAAAGGGATATTGTTCGTGGTGTAGAAGGTTTTATCGTTACTGGGTCCAAACAAGTTGAAATAGMapped 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|125054197|gb|EL125011.1|EL125011EST: ATCAGCATCAGAAGCTAGAAAAGCTTTACATATCCACTCGTGCTGCTAAG CATTACCAAAGAGA
genomic: ATCAGCATCAGAAGCTAGAAAAGCTTTACATATCCACTCGTGCTGCTAAGgttgtttttc ... tcgttttcagCATTACCAAAGAGA
EST:
gi|47831064|gb|CK120748.1|CK120748EST: ATCAGCATCAGAAGCTAGAAAAGCTTTACATATCCACTCGTGCTGCTAAG CATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGG
genomic: ATCAGCATCAGAAGCTAGAAAAGCTTTACATATCCACTCGTGCTGCTAAGgttgtttttc ... tcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtttgaagttttgattactattgattttggactcattcgttcttcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG
tattgat putative branch site (score: 3)
ttcgttcttcgttttc putative PPT
attactattgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgtttttcttaagcttttgactagtttgaagttttgattactattgattttggactcattcgttcttcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG