Sequence
atgc intronic sequence ATGC exonic sequencegtaagtataaattctctcgcgccctaatttctccaccattgatttctctaattgtactgtgtatagattatgatttcgttgaataatcttagtgcttgatgtgtttgataagatttatatgattcatgtgccaattttgatgaacagGGTTTTAGGAAAGTGGATCCAGATCGATGGGAATTTGCTAATGAAGGTTTCTTAAGAGGTCAAAAACATCTATTGAAGAAGATAAGCCGGAGAAAATCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G17750.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G17750.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g63750.1 (Oryza sativa), 3'ss of exon 1
gtaagtataaattctctcgcgccctaatttctccaccattgatttctctaattgtactgtgtatagattatgatttcgttgaataatcttagtgcttgatgtgtttgataagatttatatgattcatgtgccaattttgatgaacagGGTTTTAGGAAAGTGGATCCAGATCGATGGGAATTTGCTAATGAAGGTTTCTTAAGAGGTCAAAAACATCTATTGAAGAAGATAAGCCGGAGAAAATCTG
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---------------------------------------------atcatataacactcagtcagaagtacttgtaccgggcagatacactgtgccatgtacgttagccggcctctaacgatctcattggtgcactt--atgagcagGGATTTAGGAAAGTTGATCCAGATAGGTGGGAGTTTGCAAACGAAGGTTTTCTTAGAGGACAAAAGCATCTACTGAAGACCATCAACAGAAGGAAACCAA
upper sequence: AT4G17750.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
gtaagtataaattctctcgcgccctaatttctccaccattgatttctctaattgtactgtgtatagattatgatttcgttgaataatcttagtgcttgatgtgtttgataagatttatatgattcatgtgccaattttgatgaacagGGTTTTAGGAAAGTGGATCCAGATCGATGGGAATTTGCTAATGAAGGTTTCTTAAGAGGTCAAAAACATCTATTGAAGAAGATAAGCCGGAGAAAATCTG
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--------------------------------------------ccttaatttgatttgcactcagctgacaatcgggagagattattttctcagctaacaattatattgcgccctaacgatctcatcggtgccttcttac---cagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
upper sequence: AT4G17750.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G33920.1 (Glycine max), 3'ss of exon 2
gtaagtataaattctctcgcgccctaatttctccaccattgatttctctaattgtactgtgtatagattatgatttcgttgaataatcttagtgcttgatgtgtttgataagatttatatgattcatgtgccaattttgatgaacagGGTTTTAGGAAAGTGGATCCAGATCGATGGGAATTTGCTAATGAAGGTTTCTTAAGAGGTCAAAAACATCTATTGAAGAAGATAAGCCGGAGAAAATCTG
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-----------------------------------tctgtgttttatataacaactc-------aagctgtg-tgccttttcatatgccctgtcttttttttctcttcc----tttctaacatcgtcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAGGGGTCAAAAGCACTTGCTTAGGAGTATAACAAGACGAAAACCTG
upper sequence: AT4G17750.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G01990.1 (Glycine max), 3'ss of exon 1
gtaagtataaattctctcgcgccctaatttctccaccattgatttctctaattgtactgtgtatagattatgatttcgttgaataatcttagtgcttgatgtgtttgataagatttatatgattcatgtgccaattttgatgaacagGGTTTTAGGAAAGTGGATCCAGATCGATGGGAATTTGCTAATGAAGGTTTCTTAAGAGGTCAAAAACATCTATTGAAGAAGATAAGCCGGAGAAAATCTG
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-------------------------------------------ataacaactcaagttgtgtgccttttcagagtgtgttga----cctctgtcctgtcttttcttttttccttttctaacgtcatcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAAGGGTCAAAAGCACTTGCTTAGGAGTATTACACGACGAAAACCTG
upper sequence: AT4G17750.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G13400.1 (Glycine max), 3'ss of exon 1
gtaagtataaattctctcgcgccctaatttctccaccattgatttctctaattgtactgtgtatagattatgatttcgt-tgaataatcttagtgcttgatgtgtttgataagatttatatgattcatgtgccaattttgatgaacagGGTTTTAGGAAAGTGGATCCAGATCGATGGGAATTTGCTAATGAAGGTTTCTTAAGAGGTCAAAAACATCTATTGAAGAAGATAAGCCGGAGAAAATCTG
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-----------------------------------------tttagtttgtttgtgc-atgccaaaactataatgttgtgtatgtcaaatcaaacatcgaccttttccttt---ctaatatcatcaacaattca---tcattaagcagGGATTTAGGAAGGTAGATCCAGATCGCTGGGAATTTGCAAATGAGGGATTTTTGAGGGGTCAAAAGCACTTGCTTAAGACTATAACTCGGCGGAAACCTG
upper sequence: AT4G17750.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv02s0012g01810.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtataaattctctcgcgccctaatttctccaccattgatttctctaattgtactgtgtata-gattatgatttcgttgaataatcttagtgcttgatgtgtttgataa---gatttatatgattcatgtgccaattttgatgaacagGGTTTTAGGAAAGTGGATCCAGATCGATGGGAATTTGCTAATGAAGGTTTCTTAAGAGGTCAAAAACATCTATTGAAGAAGATAAGCCGGAGAAAATCTG
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---------------------------------------------------ttttattttgtatgtaatcaaagtctctttgtattctgctgattatagtttccctttcttccccatcctattttcctatcttgtcactgtctgcaaacagGGATTCAGGAAGGTTGATCCAGACCGTTGGGAATTTGCAAATGAGGGATTTTTGAGGGGTCAAAAACACCTATTGAGGAGTATAAATCGGCGAAAACCTGMapped 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|19877004|gb|AU237835.1|AU237835EST: ACTTCAAACACAACAATTTCTCCAGCTTTGTTCGCCAGTTAAACACCTAT GGTTTTAGGAAAGTGGATCCAGATCGATGGGAATTTGCTAATGAAGGTTTC
genomic: ACTTCAAACACAACAATTTCTCCAGCTTTGTTCGCCAGTTAAACACCTATgtaagtataa ... tgatgaacagGGTTTTAGGAAAGTGGATCCAGATCGATGGGAATTTGCTAATGAAGGTTTC
EST:
gi|86066510|gb|DR362267.1|DR362267EST: ACTTCAAACACAACAATTTCTCCAGCTTTGTTCGCCAGTTAAACACCTAT GGTTTTAGGAAAGTGGATCCAGATCGATGGGAATTTGCTAATGAAGGTTTC
genomic: ACTTCAAACACAACAATTTCTCCAGCTTTGTTCGCCAGTTAAACACCTATgtaagtataa ... tgatgaacagGGTTTTAGGAAAGTGGATCCAGATCGATGGGAATTTGCTAATGAAGGTTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttgatgtgtttgataagatttatatgattcatgtgccaattttgatgaacagGGTTTTAGGAAAGTGGATCCAGATCGATGGGAATTTGCTAATGAAGGTTTCTTAAGAGGTCAAAAACATCTATTGAAGAAGATAAGCCGGAGAAAATCTG
ttttgat putative branch site (score: 4)
tttgataagatttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtataaattctctcgcgccctaatttctccaccattgatttctctaattgtactgtgtatagattatgatttcgttgaataatcttagtgcttgatgtgtttgataagatttatatgattcatgtgccaattttgatgaacagGGTTTTAGGAAAGTGGATCCAGATCGATGGGAATTTGCTAATGAAGGTTTCTTAAGAGGTCAAAAACATCTATTGAAGAAGATAAGCCGGAGAAAATCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA