Sequence
atgc intronic sequence ATGC exonic sequence...agattcttccactatgtgcacttaatcagtcacgccgaactacttttttggccccaatattttatattatttaaatttaaccccatttctttactttcagTCTGGTTGCTGCAAGCCCCCAACAAAATGTGGATTCACATTTGTTAATCCTACTTATTGGATAAGTCCCATAGATATGTCTGCTGATATGGATTGTCTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G46700.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G46700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G11130.1 (Glycine max), 3'ss of exon 1
agattcttccactatgtgcacttaatcagtcacgccgaactacttttttggcccca----atattttatattatttaaatttaaccccatttctttact--ttcagTCTGGTTGCTGCAAGCCCCCAACAAAATGTGGATTCACATTTGTTAATCCTACTTATTGGATAAGTCCCATAGATATGTCTGCTGATATGGATTGTCTAA
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------attaaccgggattcttcaaccacgtgttatcctttcattttttgcccccattacacgttattcatctttttcctttattcctttttttcatctcatgcagTCAGGGTGCTGCAAGCCACCAACAAAATGTGGTTACACGTTTGTGAATCCAACGTATTGGATTAGCCCTATCAACACGGCAGTAGACATGGATTGCATGA
upper sequence: AT5G46700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G36610.1 (Glycine max), 3'ss of exon 2
agattcttccactatgtgcacttaatcagtcacgccgaact-acttttttggccccaatattttatattatttaaatttaaccccatttctttactt---tcagTCTGGTTGCTGCAAGCCCCCAACAAAATGTGGATTCACATTTGTTAATCCTACTTATTGGATAAGTCCCATAGATATGTCTGCTGATATGGATTGTCTAA
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----aatcaaattttaaaaaaaaaattagagactaaaaacttagttaatcattttcttttattccttttgtcttaattcctttttattttttcttctgatgcagTCAGGATGCTGCAAGCCACCAACAAAATGTGGTTACACATTTGTGAACCCAACGTATTGGATTAGCCCTATCAACACAGCAGAAGACATGGATTGCATGAMapped 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|86076906|gb|DR372663.1|DR372663EST: TCAATGCTCATCTTGATCCCATTCAA TCTGGTTGCTGCAAGCCCCCAACAAAATGTGGATTCACATTTGTTAATCCT
genomic: TCAATGCTCATCTTGATCCCATTCAAgtaagtatcc ... ttactttcagTCTGGTTGCTGCAAGCCCCCAACAAAATGTGGATTCACATTTGTTAATCCT
EST:
gi|164171570|gb|ES185242.1|ES185242EST: GATACACTTTGGCTCAAGATTTCTTCAATGCTCATCTTGATCCCATTCAA TCTGGTTGCTGCAAGCCCCCAACAAAATGT
genomic: GATACACTTTGGCTCAAGATTTCTTCAATGCTCATCTTGATCCCATTCAAgtaagtatcc ... ttactttcagTCTGGTTGCTGCAAGCCCCCAACAAAATGT
EST:
gi|164033917|gb|EL971990.1|EL971990EST: TACACTTTGGCTCAAGATTTCTTCAATGCTCATCTTGATCCCATTCAA TCTGGCTGCTGCAAGCCCCCAACAAAATGTGGATTCACATTTGTT
genomic: TACACTTTGGCTCAAGATTTCTTCAATGCTCATCTTGATCCCATTCAAgtaagtatcc ... ttactttcagTCTGGTTGCTGCAAGCCCCCAACAAAATGTGGATTCACATTTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttggccccaatattttatattatttaaatttaaccccatttctttactttcagTCTGGTTGCTGCAAGCCCCCAACAAAATGTGGATTCACATTTGTTAATCCTACTTATTGGATAAGTCCCATAGATATGTCTGCTGATATGGATTGTCTAA
atttaac putative branch site (score: 3)
ccccatttctttactt CT-rich tract
aatattttatattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agattcttccactatgtgcacttaatcagtcacgccgaactacttttttggccccaatattttatattatttaaatttaaccccatttctttactttcagTCTGGTTGCTGCAAGCCCCCAACAAAATGTGGATTCACATTTGTTAATCCTACTTATTGGATAAGTCCCATAGATATGTCTGCTGATATGGATTGTCTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - -cttccac
- - - - - - - - - cacttaa
- - - - - - - - - - - - - - - - - - - - - - tttttgg
- - - - - - - - - - - - - - - - - - - - - - - - - -ccccaat