Sequence
atgc intronic sequence ATGC exonic sequencegttggtttcaaagtcttttctgtcagagtttatatgttgatacttagcgcagagccttagcttatataattatcaatgctttttcagGCAATGGTTGCTCGTGGAGATCTTGGAGCTGAACTTCCCATTGAAGAGGTCCCGTTGTTACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G32440.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G32440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G144730_T01 (Zea mays), 3'ss of exon 6
-gttggtttcaaagtcttttctgtcagagtttatatgttgatacttagcgcagagcct-------tagctt-----atataattatcaatgctttttcagGCAATGGTTGCTCGTGGAGATCTTGGAGCTGAACTTCCCATTGAAGAGGTCCCGTTGTTACAG
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ctctagttttgataaacaaaagggaaaatatcaccatcttgtacttagttataattctactattctagtctgctagacactaagcttgaaatcttttcagGCAATGGTGGCACGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAG
upper sequence: AT1G32440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G033526_T02 (Zea mays), 3'ss of exon 6
-------gttggtttcaaagtcttttctgtcagagtttatatgttg-atacttagcgcagagccttag---cttatataatta--tcaatgctttttcagGCAATGGTTGCTCGTGGAGATCTTGGAGCTGAACTTCCCATTGAAGAGGTCCCGTTGTTACAG
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tacaggtctaggtttgataaacaaaaatgaaaataatgccatcatgtactccttagttataattctagtctcctagacactgaacttgaaatcttttcagGCAATGGTGGCGCGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAG
upper sequence: AT1G32440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G40860.1 (Glycine max), 3'ss of exon 5
------gttggtttcaaagtcttttc--tgtcagagtttatatgttgatacttagc-gcag--agc-cttagcttatat-aattatcaatgctttttcagGCAATGGTTGCTCGTGGAGATCTTGGAGCTGAACTTCCCATTGAAGAGGTCCCGTTGTTACAG
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ttgatggaagtctttgaatgttattcaatatcaaggatcgaagcaagatctttatctacaggtagcatccggttcatcttgagttttatttattttgcagGCCATGGTCGCTCGTGGGGATCTTGGAGCTGAACTTCCAATAGAGGAAGTTCCTTTATTGCAG
upper sequence: AT1G32440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv02s0012g01170.t01 (Vitis vinifera), 3'ss of exon 6
--------------gttggtttcaaagtcttttctgtcagagtttatatgttgatacttagcgcagagccttagcttatataattatcaatgctttttcagGCAATGGTTGCTCGTGGAGATCTTGGAGCTGAACTTCCCATTGAAGAGGTCCCGTTGTTACAG
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gttagggtacttatctttttgggaaaattgctgcaactcacctttattttttgggtcatcatggtcaactgaatcttaattggttgttt-tgattgtatagGCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAG
upper sequence: AT1G32440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S205_25V6.1 (Physcomitrella patens), 3'ss of exon 5
-------gttggtttcaaagtcttttctgtcagagtttatatgttgatacttagcgcagagccttagc--ttatataattatcaa-tgcttt---ttcagGCAATGGTTGCTCGTGGAGATCTTGGAGCTGAACTTCCCATTGAAGAGGTCCCGTTGTTACAG
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actttatgcatgtgtaaggtcatgttttgcacatcatcacgaaacgcattttggtacagtgtgagcgccatattaaaattttcaactgttttcctttcagGCTATGGTTGCTCGAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgttgatacttagcgcagagccttagcttatataattatcaatgctttttcagGCAATGGTTGCTCGTGGAGATCTTGGAGCTGAACTTCCCATTGAAGAGGTCCCGTTGTTACAG
tgttgat putative branch site (score: 4)
tgctttttc putative PPT
ttatataattatcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtttcaaagtcttttctgtcagagtttatatgttgatacttagcgcagagccttagcttatataattatcaatgctttttcagGCAATGGTTGCTCGTGGAGATCTTGGAGCTGAACTTCCCATTGAAGAGGTCCCGTTGTTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG