Sequence
atgc intronic sequence ATGC exonic sequencegtgaggattctactcctgcaatatcttcatttttcttatcttaataatcactagaatgttttctttaagaataataatatccttttaatggtatgtgtatcgatttgtctttttttttcagCCTTCACTCCCAGCTAAAGACACAAGCTGTGAATCGGTGGTGACGAGTGGTCAGCACCAATTGGCATCTCAAAATCCTCAGAGAGATGCTAGTCCTGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52150.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52150.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G21610.1 (Glycine max), 3'ss of exon 3
gtgaggattctactcctgcaatatcttcatttttcttatcttaataatcactagaatgt-tttctttaagaataataatatccttttaatggtatgtgtatcgatttgtctttttttttcagCCTTCACTCCCAGCTAAAGACACAAGCTGTGAATCGGTGGTGACGAGTGGTCAGCACCAATTGGCATCTCAAAATCCTCAGAGAGATGCTAGTCCTGCAG
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-------------------tgtgcgcttaatttt-tcgtctgcccttttatgtatatatatatatatatatatatgtgaatgctttaga--atttgagttagaatggtgcttttatttgcagACAACGCAGGCAACCAAAGACACAAACTGTGAATCAGTTGTGACGAGTGGTCAGCACAATTTGACAACTCAACATCCCCCACGGGATGCAAGTCCTGCAG
upper sequence: AT1G52150.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G01950.1 (Glycine max), 3'ss of exon 2
-----------------------------------gtgag-gattctactcctgcaatatcttcatttttcttatcttaataatcactagaatgttttctttaagaataataatatccttttaatggtatgtgtatcgatttgtctttttttttcagCCT---TCACTCCCAGCTAAAGACACAAGCTGTGAATCGGTGGTGACGAGTGGTCAG---CACCAATTGGCATCTCAAAATCCTCAGAGAGATGCTAGTCCTGCAG
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gtaagaatctactactctgtttttttattgggtttgtaattaatgatgcccaatccaaatattcaatctt-ttatttgtatagttttggtaaattgttcttctacgctttcatagatttttctatgtgaaaattatagaatggcgctttctctgcagACTAAGCAGCAGCCAACCAAAGACACAAGCTGTGAATCAGCTGTGACGAGTGGTCAGCAGCACAATTTGACAACTCAACATCCCCCACGGGATGCAAGTC------
upper sequence: AT1G52150.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G01940.1 (Glycine max), 3'ss of exon 2
gtgaggattctactcctgcaatatcttcatttttcttatcttaataatcactagaatgttttctttaagaataataatatccttttaatggtatgtgtatcgatttgtctttttttttcagCCTTCACTCCCAGCTAAAGACACAAGCTGTGAATCGGTGGTGACGAGTGGTCAGCACCA---ATTGGCATCTCAAAATCCTCAGAGAGATGCTAGTCCTGCAG
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-----------------gtagttttagcaaattgcgcgcttaattgttcatc----tacccttttatagtttttctgtgtgagtgctttagaattgagttagaatggtgctttatttgcagACTACGCAGGCAACCAAAGACACAAACTGTGAATCAGTTGTGACGAGTGGTCAGCAGCACAATTTGATAACTCAACATCCCCCACGGGATGCAAGTCCTG---
upper sequence: AT1G52150.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0002g03740.t01 (Vitis vinifera), 3'ss of exon 2
gtgaggattctactcctgcaatatcttcatttttcttatcttaataatcactagaatgttttctttaagaataataatatccttttaatggtatgtgtatcgatttgtctttttttttcagCCTTCACTCCCAGCTAAAGACACAAGCTGTGAATCGGTGGTGACGAGTGGTCAGCACCAATTGGCATCTCAAAATCCTCAGAGAGATGCTAGTCCTGCAG
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-------------------cccttttttttctttcataatgctgtagttgttgtcttttgtttttacttttgaattatctgggttttttgatgcggttgttttcttggcattcttg--cagACAACGCTTGCCACAAAAGACACAAGTTGTGAGTCGGTGGTGACGAGCGGTCAACACCACTTGACCCCTCAGCATCCGCCCAGGGATGCTAGTCCTGCAGMapped 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|86068368|gb|DR364125.1|DR364125EST: TGTCACAGCTGGTCCATGAAAACAGCTACTTCCGTCAACATACTCCCAAT CCTTCACTTCCAGCTAAAGACACAAGCTGTGAATCGGTGGTGACGAGTGGT
genomic: TGTCACAGCTGGTCCATGAAAACAGCTACTTCCGTCAACATACTCCAAATgtgaggattc ... tttttttcagCCTTCACTCCCAGCTAAAGACACAAGCTGTGAATCGGTGGTGACGAGTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagaataataatatccttttaatggtatgtgtatcgatttgtctttttttttcagCCTTCACTCCCAGCTAAAGACACAAGCTGTGAATCGGTGGTGACGAGTGGTCAGCACCAATTGGCATCTCAAAATCCTCAGAGAGATGCTAGTCCTGCAG
ttttaat putative branch site (score: 3)
tttgtctttttttttc putative PPT
taataatatcctttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggattctactcctgcaatatcttcatttttcttatcttaataatcactagaatgttttctttaagaataataatatccttttaatggtatgtgtatcgatttgtctttttttttcagCCTTCACTCCCAGCTAAAGACACAAGCTGTGAATCGGTGGTGACGAGTGGTCAGCACCAATTGGCATCTCAAAATCCTCAGAGAGATGCTAGTCCTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG