Sequence
atgc intronic sequence ATGC exonic sequencegtaaggactcttttacctgtatatagattatgagaatctgctctttgttttctgccaattactggtgctgagaagtttgctatttcttttgttgttttgaagGTTAGAAGAGAAAAGATCAGTGAAAGGATGAGATTGCTTCAAGAACTTGTTCCCGGATGCAACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G10120.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G10120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G10180.1 (Glycine max), 3'ss of exon 2
gtaaggactcttttacctgtatatagattatga-gaatctgctctttgttttctgccaattactggtgctgagaagtttgctatttcttttgttgttttgaagGTTAGAAGAGAAAAGATCAGTGAAAGGATGAGATTGCTTCAAGAACTTGTTCCCGGATGCAACAAG
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gtaccatccctatc-tcaaaatatttgttatgataaagttagaaaatccctttttttttttgtatgt-ctaatga---tacaacttttttgcttgc-----agGTGAGAAGAGAAAAGATTAGTGAGCGAATGAGGTTGCTTCAAGAACTTGTTCCAGGATGCAACAAG
upper sequence: AT1G10120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA0041S00210.1 (Glycine max), 3'ss of exon 2
----------------gtaaggactcttttacctgtatatagattatgagaatctgctctttgttttctgccaattactggtgctgagaagtttg----ctatttcttttgttgt-----------------------tttgaagGTTAGAAGAGAAAAGATCAGTGAAAGGATGAGATTGCTTCAAGAACTTGTTCCCGGATGCAACAAG
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gtgagagctagaagaggtcaagccactaacagccacagccttgcagaaagagtaccatccctatctcaccacgatatttgctatgagaaagttagaaaacccttttttttgttgtatgtctaatgatacaactttttgctcgcagGTGAGAAGAGAAAAGATTAGTGAGCGAATGAGGTTGCTTCAAGAACTTGTTCCAGGTTGCAACAAG
upper sequence: AT1G10120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G05180.1 (Glycine max), 3'ss of exon 3
gtaaggactcttttacctgtatatagattatgagaatctgctctttgttttctgccaattactggtgctgagaagtttgctatttcttttgttgttttgaagGTTAGAAGAGAAAAGATCAGTGAAAGGATGAGATTGCTTCAAGAACTTGTTCCCGGATGCAACAAG
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------------gtaccatcatcttaac-acataaatctttgttacgagaaac-ccattttttattgataaagtatgagttataacacactcatgtttgcagGTAAGGAGAGAAAAGATTAGTGAGCGAATGAGGTTGCTTCAAGAACTTGTTCCAGGATGCGAAAAG
upper sequence: AT1G10120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G05090.1 (Glycine max), 3'ss of exon 4
gtaaggactcttttacctgtatatagat-tatgagaatctgctctttgttttctgccaattactggtgctgagaagtttgctatttcttttgttgttttgaagGTTAGAAGAGAAAAGATCAGTGAAAGGATGAGATTGCTTCAAGAACTTGTTCCCGGATGCAACAAG
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-----------gtaaccatcatcttaacacattaatgtttattactagaaacccgctttttattgataaattagagtt-ataacactttttgtt----tgcagGTGAGGAGAGAAAAGATTAGTGAGCGAATGAGGTTACTTCAAGAACTTGTTCCAGGATGCGATAAG
upper sequence: AT1G10120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0001g08600.t01 (Vitis vinifera), 3'ss of exon 2
gtaaggactcttttacctgtatatagattatgagaatctgctctttgttttctgccaattactggtgctgagaagtttgctatttcttttgttgttttgaagGTTAGAAGAGAAAAGATCAGTGAAAGGATGAGATTGCTTCAAGAACTTGTTCCCGGATGCAACAAG
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-----gtatcttcttgctat-tatgcatta----aatgttatgaaagacctctgctttctgatg-tatcttgaacctagatgttttat------gtttgcagGTCAGAAGAGAAAAGATCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTTCCAGGATGTAATAAGMapped 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|19876968|gb|AU237799.1|AU237799EST: TGAGGGCAAGAAGAGGTCAAGCCACTAATAGTCACAGTCTTGCAGAGCGG GTTAGAAGAGAAAAGATCAGTGAAAGGATGAGATTGCTTCAAGAACTTGTT
genomic: TGAGGGCAAGAAGAGGTCAAGCCACTAATAGTCACAGTCTTGCAGAGCGGgtaaggactc ... tgttttgaagGTTAGAAGAGAAAAGATCAGTGAAAGGATGAGATTGCTTCAAGAACTTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttctgccaattactggtgctgagaagtttgctatttcttttgttgttttgaagGTTAGAAGAGAAAAGATCAGTGAAAGGATGAGATTGCTTCAAGAACTTGTTCCCGGATGCAACAAG
tttcttttgttgtttt CT-rich tract
tatttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggactcttttacctgtatatagattatgagaatctgctctttgttttctgccaattactggtgctgagaagtttgctatttcttttgttgttttgaagGTTAGAAGAGAAAAGATCAGTGAAAGGATGAGATTGCTTCAAGAACTTGTTCCCGGATGCAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC