Sequence
atgc intronic sequence ATGC exonic sequencegtactctatctagagtcatgtcataactattttattttctttctgatgactaatgctgacttttaattggcttacagCGAAGTTAGTGGAGACCGTGAGGTACAAAGGACAATGTTGGAGCTGCTCAACCAGCTTGATGGATTCAGCAGCGATGATCGCATTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G09100.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 6
-------------gtactctatctagagtcatgtcataactattttattttctttctg-atga-----ctaatgctgacttttaattggctt----acagCGAAGTTAGTGGAGACCGTGAGGTACAAAGGACAATGTTGGAGCTGCTCAACCAGCTTGATGGATTCAGCAGCGATGATCGCATTAAG
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catacgatgtgttctcctttactaattaacttgtgagcacaattgctttttgtgagtgcaagagtctcctaatatttttctttgtttcattttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAACCAGCTTGATGGATTTAGCAGCGATGAGAGGATAAAG
upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------gtactctatctagagtcatgtcataactattttattttctttctgatgactaatgctgacttttaattggcttacagCGAAGTTAGTGGAGACCGTGAGGTACAAAGGACAATGTTGGAGCTGCTCAACCAGCTTGATGGATTCAGCAGCGATGATCGCATTAAG
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gtattagctggcaaaaaattagatatacatttgcaattgacttttttttcccccctctagagaga---ctcaggtaaaatatagtggttccaacc-ttgatg-tatcttgtggctga-ttgcagTGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATTAAG
upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------------------------------------gtactct-atctagagtcatgtcataactattttattttctttctgatgact-aatgctgacttttaattggcttacagCGAAGTTAGTGGAGACCGTGAGGTACAAAGGACAATGTTGGAGCTGCTCAACCAGCTTGATGGATTCAGCAGCGATGATCGCATTAAG
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gtttgtaatgttctcttcaaagtgtctatacagaacatcttgtagagcgtttttagaggaagggtacacttatcttggtcaaattgattatattatgacaatcttatttgtgacttgatcttcggtttatgttggc----agTGAAGTAAGTGGAGATCGTGAAGTGCAGAGAACTATGCTGGAGTTGCTTAATCAGCTGGATGGATTCAGCAGTGATGAGCGCATTAAAMapped 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|164211878|gb|ES109756.1|ES109756EST: GGGACAAAGCGTTTTGATAG CGAAGTTAGTGGAGACCGTGAGGTACAAAGGACAATGTTGGAGCTGCTCAA
genomic: GGGACAAAGCGTTTTGATAGgtactctatc ... tggcttacagCGAAGTTAGTGGAGACCGTGAGGTACAAAGGACAATGTTGGAGCTGCTCAA
EST:
gi|164125758|gb|ES164010.1|ES164010EST: GACGCAATAGGGACAAAGCGTTTTGATAG CGAAGTTAGTGGAGACCGTGAGGTACAAAGGACAATGTTGGAGCTGCTCAA
genomic: GACGCAATAGGGACAAAGCGTTTTGATAGgtactctatc ... tggcttacagCGAAGTTAGTGGAGACCGTGAGGTACAAAGGACAATGTTGGAGCTGCTCAA
EST:
gi|164138078|gb|ES015529.1|ES015529EST: ATTATATTCATAGATGAGATTGACGCAATAGGGACAAAGCGTTTTGATAG CGAAGTTAGTGGAG
genomic: ATTATATTCATAGATGAGATTGACGCAATAGGGACAAAGCGTTTTGATAGgtactctatc ... tggcttacagCGAAGTTAGTGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataactattttattttctttctgatgactaatgctgacttttaattggcttacagCGAAGTTAGTGGAGACCGTGAGGTACAAAGGACAATGTTGGAGCTGCTCAACCAGCTTGATGGATTCAGCAGCGATGATCGCATTAAG
tattttattttctttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactctatctagagtcatgtcataactattttattttctttctgatgactaatgctgacttttaattggcttacagCGAAGTTAGTGGAGACCGTGAGGTACAAAGGACAATGTTGGAGCTGCTCAACCAGCTTGATGGATTCAGCAGCGATGATCGCATTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA