Sequence
atgc intronic sequence ATGC exonic sequencegtatagtatctgaattactttattttagatatattctctacatattctttcttgcctttatagtaccttgatattttattactccatacagGAAGCTGTGGGTAAAAAAGGTATTCGTGATGATACAACCTGTATTGTTGTTGATATATTGCCACTAGAAAAACCGGCTGCTTCCGTGCCGCCTCCAAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G47380.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G052699_T01 (Zea mays), 3'ss of exon 6
gtatagtatctgaattactttattt-tagatatattctctacatattctttcttgcctttatagtaccttgatattttattactccatacagGAAGCTGTGGGTAAAAAAGGTATTCGTGATGATACAACCTGTATTGTTGTTGATATATTGCCACTAGAAAAACCGGCTGCTTCCGTGCCGCCTCCAAAAA---
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-------------gtaacctcctttctatgtgcagcca-taaatcttgaatgatactcttat-----ttacatatctga--aacttttgcagACTGCTGTGCAATCAAAAGGGCTGAGGGATGATACCACCTGTATTGTTGTTGATATAATAGTA--GAAAAAAACAACT-CTTCCATGCCACTTGCTAAAAGGC
upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G052699_T02 (Zea mays), 3'ss of exon 5
--gtata-gtatctgaattactttattttagatatattctctacatattctttcttg---cctttatagtaccttgat----attttattactccatacagGAAGCTGTGGGTAAAAAAGGTATTCGTGATGATACAACCTGTATTGTTGTTGATATATTGCCACTAGAAAAACCGGCTGCTTCCGTGCCGCCTCCAAAAA---
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cagtgcctgcagctgagcaaatc-gttaaagtaacctcctttctatgtgcagccataaatcttgaatgatactcttatttacatatctgaaacttttgcagACTGCTGTGCAATCAAAAGGGCTGAGGGATGATACCACCTGTATTGTTGTTGATATAATAGTA--GAAAAAAACAACT-CTTCCATGCCACTTGCTAAAAGGC
upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G081359_T02 (Zea mays), 3'ss of exon 3
----------------gtatagtatctgaattactttattttagatatattctctacatattctttcttgcctttatagtaccttgatattttattactccatacagGAAGCTGTGGGTAAAAAAGGTATTCGTGATGATACAACCTGTATTGTTGTTGATATATTGCCACTAGAAAAACCGGCTGCTTCCGTGCCGCCTCCAAAAA---
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cagtgcctgcagctgagcaaatcgt-taaagtaacttgcttttgatgtgcagcctaaatcctgaatgatacagttat-----ttacatatctgaaaccttc-tgcagACTGCTGTGCAATCAAAAGGACTGAGGGATGATACCACCTGTATTGTTGTTGATATAATAGCA--GAGAAAACCAACC-CTTCCATGCCACTTCCTAGAAGGC
upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G081359_T01 (Zea mays), 3'ss of exon 5
gtatagtatctgaattactttattttagatatattctctacatattctttcttgcctttatagtaccttgatattttattactccatacagGAAGCTGTGGGTAAAAAAGGTATTCGTGATGATACAACCTGTATTGTTGTTGATATATTGCCACTAGAAAAACCGGCTGCTTCCGTGCCGCCTCCAAAAA---
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--------------gtaacttgcttttgatgtgcagcctaaatcctgaatgatacagttat-----ttacatatctgaaaccttc-tgcagACTGCTGTGCAATCAAAAGGACTGAGGGATGATACCACCTGTATTGTTGTTGATATAATAGCA--GAGAAAACCAACC-CTTCCATGCCACTTCCTAGAAGGCMapped 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|124819791|gb|EH904657.1|EH904657EST: ATTGTTGCCGGGGGTTGCCACCTGAATCTTCTGCGGAGCATATCGTTAAA GAAGCTGTGGGTAAAAA-GGTATTCGTGATGATACAACCTGTAT
genomic: ATTGTTGCCGGGGGTTGCCACCTGAATCTTCTGCGGAGCATATCGTTAAAgtatagtatc ... ctccatacagGAAGCTGTGGGTAAAAAAGGTATTCGTGATGATACAACCTGTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctacatattctttcttgcctttatagtaccttgatattttattactccatacagGAAGCTGTGGGTAAAAAAGGTATTCGTGATGATACAACCTGTATTGTTGTTGATATATTGCCACTAGAAAAACCGGCTGCTTCCGTGCCGCCTCCAAAAA
ccttgat putative branch site (score: 5)
ttactcc putative PPT
ttgatattttattact 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
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gtatagtatctgaattactttattttagatatattctctacatattctttcttgcctttatagtaccttgatattttattactccatacagGAAGCTGTGGGTAAAAAAGGTATTCGTGATGATACAACCTGTATTGTTGTTGATATATTGCCACTAGAAAAACCGGCTGCTTCCGTGCCGCCTCCAAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT