Sequence
atgc intronic sequence ATGC exonic sequencegtgtgattctttgtttttatgttctttggtttcaactcaaaatgcagaattttgattaacaattatctatggacaatgttatgttacagGATGTTGCTATGGCATTGTTGTTTGGAATAGGATACGCTGGCATCATCTTTGAAGAGTCTTTAGCTTTTAATAAAAGTGGAATAGGACTTTTGATGGCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G19490.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G19490.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G40920.1 (Glycine max), 3'ss of exon 2
----------------------------------gtgtgattctttgtttt-tatgttctttggtttcaa---ctcaaaatgcagaattttgattaacaattatctatggacaatgttatgttacagGATGTTGCTATGGCATTGTTGTTTGGAATAGGATACGCTGGCATCATCTTTGAAGAGTCTTTAGCTTTTAATAAAAGTGGAATAGGACTTTTGATGGCTG
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gtacttcaatgtcctctatcctgatttcaatgctgcacatttcatagtgaagtacgtgtattagggaaaatatctctaaatatgcatattctaatagttatttgttttccatgacattggactgtagGATCTTGCTATGGCATTGCTATTTGTAATAGGATATGCAGGCATCATATTTGAAGAATCTCTAGCCTTCAATAAAAGTGGAGTGGGACTGTTGATGGCTG
upper sequence: AT3G19490.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G26380.1 (Glycine max), 3'ss of exon 2
----------------------------------gtgtgattctttgtt---tttatgttctttggttt-caactcaaaatgcagaattttgattaacaattatctatggacaatgttatgttacagGATGTTGCTATGGCATTGTTGTTTGGAATAGGATACGCTGGCATCATCTTTGAAGAGTCTTTAGCTTTTAATAAAAGTGGAATAGGACTTTTGATGGCTG
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gtacttcaatgtcctctatcctgatttcaatgctgcacatttcacaatgaagtacatgtactagggaaaatgcctctaaatatgcatattctaatagttatttgttttctatgacatttgactgtagGATCTTGCTATGGCATTGCTATTTGTAATAGGATATGCAGGCATCATATTTGAAGAATCTCCAGCCTTCAATAAAAGTGGAGTGGGACTGTTGATGACTG
upper sequence: AT3G19490.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv03s0180g00120.t01 (Vitis vinifera), 3'ss of exon 2
------------------gtgtgattcttt-----gtttttatgttctttg----gtttcaactcaaaatgcagaattttgattaacaattatctatggacaa------tgttatgttacagGATGTTGCTATGGCATTGTTGTTTGGAATAGGATACGCTGGCATCATCTTTGAAGAGTCTTTAGCTTTTAATAAAAGTGGAATAGGACTTTTGATGGCTG
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gtccattttcatcttgttgtctgattcttttgatggttttcttgtttgcttacatgcctttgttaaaaaaagttcatacgaataaaggggcattacaaaacaaatcagttctcatgatatagGATGCTGCTATGGCATTGCTATTTGGAGTGGGATATGCTGGAATAATTTTTGAAGAATCTCTAGCCTTTAACAAAAGTGGAGTGGGGTTATTGATGGCTGMapped 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|164008858|gb|ES170959.1|ES170959EST: CCTGGGTCGCTGCTAATCAG GATGTTGCTATGGCATTGTTTGTTTGGAATAGGATACGCTGGCATCATCTT
genomic: CCTGGGTCGCTGCTAATCAGgtgtgattct ... tatgttacagGATGTTGCTATGGCATTG-TTGTTTGGAATAGGATACGCTGGCATCATCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actcaaaatgcagaattttgattaacaattatctatggacaatgttatgttacagGATGTTGCTATGGCATTGTTGTTTGGAATAGGATACGCTGGCATCATCTTTGAAGAGTCTTTAGCTTTTAATAAAAGTGGAATAGGACTTTTGATGGCTG
gattaac putative branch site (score: 2)
aattttgattaacaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgattctttgtttttatgttctttggtttcaactcaaaatgcagaattttgattaacaattatctatggacaatgttatgttacagGATGTTGCTATGGCATTGTTGTTTGGAATAGGATACGCTGGCATCATCTTTGAAGAGTCTTTAGCTTTTAATAAAAGTGGAATAGGACTTTTGATGGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA