Sequence
atgc intronic sequence ATGC exonic sequencegttcagtatgtcttgattttcgtagcttagatgatctgattttgtgtagatattttgattcagcgagctctatagtagtagcctttaggaatcgatctgttaatgtatgtgttgttgattggtagtatcatttttggtgtggtgaagGTAGGTATTTGAAATGGCGACAGTTCCAGGACAATTGATCTGGGAGATCGTGAAGAACAACAACTGTTTCTTGGTGAAGCAGTTCGGTAGAGGAAACTCT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G19730.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G19730.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g46430.2 (Oryza sativa), 3'ss of exon 1
gttcagtatgtcttgattttcgtagcttagatgatctgattttgtgtagatattttgattcagcgagc-tctatagtagtagcctttaggaatcgatctgttaatgtatgtgttgttgattggtagtatcatttttggtgtggtgaagGTAGGTATTTGAAATGGCGACAGTTCCAGGACAATTGATCTGGGAGATCGTGAAGAACAACAACTGTTTCTTGGTGAAGCAGTTCGGTAGAGGAAACTCT---
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--------------------------------------------ggcaaatgttgcgttataataatcatatatatgggtcactttttcctgctgatcattagttacaggatcttacagtaggt--tgttggttttggttatgtagGCGAAG-----CGAAATGGCGACGGTTCCGGAGCCTTTGATCTGGGAGATTGTCAAGAAGAACAACTGCTTCCTGGTGAAGCAGTTCGGGAATAGCAATGCCAAG
upper sequence: AT2G19730.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g57540.1 (Oryza sativa), 3'ss of exon 1
gttcagtatgtcttgattttcgtagcttagatgatctgattttgtgtagatattttgattcagcgagctctatagtagtagcctttaggaatcgatctgttaatgtatgtgttgttgattggtagtatcatttttggtgtggtgaagGTAGGTATTTGAAATGGCGACAGTTCCAGGACAATTGATCTGGGAGATCGTGAAGAACAACAACTGTTTCTTGGTGAAGCAGTTCGGTAGAGGAAACTCT---
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-------------------------------------------ttgctgccagcgttgtgtaatg--tttttgcgtgttaatggtcacttagtggtctgatggt-catttgctatggtgtaatggt-cgatctgtttggtgatgtagCTACAG---CGAAATGGCGACGGTTCCGGAGCCTTTGTTCTGGGAGATTGTGAAGAAGAACAACTGCTTCCTCGTGAAGCAGTTTGGAAACAGCAATGCCAAG
upper sequence: AT2G19730.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G088060_T02 (Zea mays), 3'ss of exon 2
gttcagtatgtcttgattttcgtagcttagatgatctgattttgtgtagatattttgattcagcgagctctatagt-agtagcctttaggaatcgatctgttaatgtatgtgttgttgattggtagtatcatttttggtgtggtgaagGTAGGTATTTGAAATGGCGACAGTTCCAGGACAATTGATCTGGGAGATCGTGAAGAACAACAACTGTTTCTTGGTGAAGCAGTTCGGTAGAGGAAACTCT---
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-----------------------------------------aaccgtaactattcc---ccagatggtcaggtgatcagttttctccctgtttaatgttgcaagggaatctcacatttgccagt--tgatattttcgactatttagGCGAAGG-----GAAATGGCGACCGTTCCAGGGGATCTGATCTGGCAGATTGTGAGGAAGAACAACTCCTTCCTGGTGAAGCAGTTTGGCAACGGCAATGCCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgatctgttaatgtatgtgttgttgattggtagtatcatttttggtgtggtgaagGTAGGTATTTGAAATGGCGACAGTTCCAGGACAATTGATCTGGGAGATCGTGAAGAACAACAACTGTTTCTTGGTGAAGCAGTTCGGTAGAGGAAACTCT
tatcattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcagtatgtcttgattttcgtagcttagatgatctgattttgtgtagatattttgattcagcgagctctatagtagtagcctttaggaatcgatctgttaatgtatgtgttgttgattggtagtatcatttttggtgtggtgaagGTAGGTATTTGAAATGGCGACAGTTCCAGGACAATTGATCTGGGAGATCGTGAAGAACAACAACTGTTTCTTGGTGAAGCAGTTCGGTAGAGGAAACTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA