Sequence
atgc intronic sequence ATGC exonic sequencegtttctattttcattactattttctattgtggctttgattcatgaacccagctcgattctctggttgatttttttgttgcaatgtggtgttgatattggaaaggattggtttttgacctgtgggtgattcatattagGTTGTTAGGGCAAAGAAGAAGGAAACTGGAACTGTGTATGCTTTAAAGATTATGGACAAAAAGTTTATCACCAAGGAGAATAAAACTGCTTATGTGAAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G04510.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04510.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g65230.1 (Oryza sativa), 3'ss of exon 1
gtttctattttcattactattttctattgtggctttgattcatgaacccagctcgattctctggttgatttttttgttgcaatgtggtgttgatattggaaaggattggtttttgacctgtgggtgattcatattagGTTGTTAGGGCAAAGAAGAAGGAAACTGGAACTGTGTATGCTTTAAAGATTATGGACAAAAAGTTTATCACCAAGGAGAATAAAACTGCTTATGTGAAAT
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----------------------------gtg-ttttgatttgattgatcggttcgcatgcgatgatgccccctgatcatccgcgttctcgtggttcttgtgcctggtggtgtc--attcatggtggaatt-tggcagGTGGTGAGGGCCAAGAAGAAGGATACGGGGAATGTGTACGCGCTCAAGATCATGGACAAGAAGTTCATCACCAAGGAGAACAAGATCTCCTACGTCAAGA
upper sequence: AT5G04510.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G33140.1 (Glycine max), 3'ss of exon 1
gtttctattttcattactattttctattgtggctttgattcatgaacccagctcgattctctggttgatttttttgttgcaatgtggtgttgatattggaaaggattggtttttgacctgtgggtgattcatattagGTTGTTAGGGCAAAGAAGAAGGAAACTGGAACTGTGTATGCTTTAAAGATTATGGACAAAAAGTTTATCACCAAGGAGAATAAAACTGCTTATGTGAAAT
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---------------------------tggaacttttttttttg---------ctattatgtggtgaacagttgtttgagtgtatttattttctcttgtaaatcatcaccaaatatcttacttattatgtttaa-agGTTGTGAGGGCAAAGAAGAAGGACACTGGAACTGTGTATGCATTGAAGATCATGGACAAAAAATTTATTACCAAAGAGAATAAAACAGCTTATGTGAAGT
upper sequence: AT5G04510.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G34430.1 (Glycine max), 3'ss of exon 1
gtttctattttcattactattttctattgtggctttgattcatgaacccagctcgattctctggttgatttttttgttgcaatgtggtgttgatattggaaaggattggtttttgacctgtgggtgattcatattagGTTGTTAGGGCAAAGAAGAAGGAAACTGGAACTGTGTATGCTTTAAAGATTATGGACAAAAAGTTTATCACCAAGGAGAATAAAACTGCTTATGTGAAAT
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------------------acttttttttccc-ctctgttatatatgctgaaca-gttgtttgagtggatttatctactcttgtaaattatcacca---------aatatctttcttcttatgtttaa--------agGTTGTGAGGGCAAAGAAGAAGGACACTGGAATTGTGTACGCATTGAAGATCATGGACAAAAAATTTATTACCAAAGAGAACAAAACAGCTTATGTGAAGT
upper sequence: AT5G04510.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0074g00100.t01 (Vitis vinifera), 3'ss of exon 2
gtttctattttcattactattttctattgtggctttgattcatgaacccagctcgattctctggttgattttt-ttgttgcaatgtggtgttgatattggaaaggattggtttttgacctgtgggtgattcatattagGTTGTTAGGGCAAAGAAGAAGGAAACTGGAACTGTGTATGCTTTAAAGATTATGGACAAAAAGTTTATCACCAAGGAGAATAAAACTGCTTATGTGAAAT
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-----------------------------------tggg-cacttacgcatctggaattgatgtctggttttaattgttagcatttgggtatgtggttatttat--ttgtttctttattttatatcaattgactccagGTTGTGAGGGCAAGGAAGAAGGACACTGGAATTGTGTACGCTTTGAAAATCATGGACAAAAAGTTCATCACAAAAGAAAATAAAACAGCTTATGTGAAGTMapped 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|116381741|gb|EG424333.1|EG424333EST: GCCATGATTTCGAATTTGGCAAGATCTATGGTGTTGGTTCTTACTCTAAG GTTGTTAGGGCAAAGAAGAAGGAAACTGGAACTGTGTATGCTTTAAAGATT
genomic: GCCATGATTTCGAATTTGGCAAGATCTATGGTGTTGGTTCTTACTCTAAGgtttctattt ... ttcatattagGTTGTTAGGGCAAAGAAGAAGGAAACTGGAACTGTGTATGCTTTAAAGATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtggtgttgatattggaaaggattggtttttgacctgtgggtgattcatattagGTTGTTAGGGCAAAGAAGAAGGAAACTGGAACTGTGTATGCTTTAAAGATTATGGACAAAAAGTTTATCACCAAGGAGAATAAAACTGCTTATGTGAAAT
ttttgac putative branch site (score: 3)
attcatatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttctattttcattactattttctattgtggctttgattcatgaacccagctcgattctctggttgatttttttgttgcaatgtggtgttgatattggaaaggattggtttttgacctgtgggtgattcatattagGTTGTTAGGGCAAAGAAGAAGGAAACTGGAACTGTGTATGCTTTAAAGATTATGGACAAAAAGTTTATCACCAAGGAGAATAAAACTGCTTATGTGAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA