Sequence
atgc intronic sequence ATGC exonic sequencegtatggtactatccttgatacgttatcccttgtcagacggtgtttggcatatgcatactgaattgtagataatcagatacttgtctctacagGATATGTTTGAGGAGAAACGGAACATATTGGAACCAGCAGGGGCTCTTGCACTCGCTGGAGCTGAGGCATACTGTAAATATTATGGCCTAAAGGACGTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G10050.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G10050.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g50510.1 (Oryza sativa), 3'ss of exon 4
-------gtatggtactatcc--ttgatacgttatcccttgtcagacggtgtttggcatatgca-tactgaattgtagataatcagatacttgtctctacagGATATGTTTGAGGAGAAACGGAACATATTGGAACCAGCAGGGGCTCTTGCACTCGCTGGAGCTGAGGCATACTGTAAATATTATGGCCTAAAGGACGTGA
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ggtgctaggaatctatgatcggactactgctatattccaatcttacccttataatgcttctgcggttctgccctataattttttt--tggtcatggctgcagGATATGTTTGAGGAGAAAAGAAGCATACTTGAACCTGCTGGTGCCCTTGCGCTGGCAGGAGCTGAAGCTTACTGCAAATACTATGGCTTGAAAGGGGAAA
upper sequence: AT3G10050.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G21230.1 (Glycine max), 3'ss of exon 4
--gtatggtactatccttgatacgt-tatcccttgtcagacggtg----tttggcatatgcatactgaattgtagataatcaga-tacttgtctctacagGATATGTTTGAGGAGAAACGGAACATATTGGAACCAGCAGGGGCTCTTGCACTCGCTGGAGCTGAGGCATACTGTAAATATTATGGCCTAAAGGACGTGA
| || | || || || || | || || || | || | | | | | || | ||| || | | ||||||||||| ||||||||| |||||||||| ||||||||||| || |||||||| |||||||||||||||||||| || || |||| | ||| |
ttacgcagacctttgattatctagtacatttaatgcaaaacagtacagattctgtatgacttaattttttgggatatgacaagaataaaacttgttgcagGATATGTTCGAGGAGAAAAGGAACATATTAGAACCAGCAGGAGCACTTGCACTAGCTGGAGCTGAGGCATACTGCAAGCATCATGGGATCCAGGGGAAAA
upper sequence: AT3G10050.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G07340.1 (Glycine max), 3'ss of exon 4
gtatggtactatccttgata----cgttatcccttg--tcagacggtgtt-tggcatatgcatactgaattgtagataatcaga-tacttgtctctacagGATATGTTTGAGGAGAAACGGAACATATTGGAACCAGCAGGGGCTCTTGCACTCGCTGGAGCTGAGGCATACTGTAAATATTATGGCCTAAAGGACGTGA
| | | || | |||| | | | || || | ||| | | |||| | | |||| | || | ||| || | | ||||||||||| ||||||||| |||||||||| ||||||||||| || |||||||| |||||||||||||||||||| || || |||| | |||
ctgttgctctgttgttgacattctctctgtctctaggttcataggctgttgtaatgaaaagcagtaaaattttgtatgacaagaataaaacttgttgcagGATATGTTCGAGGAGAAAAGGAACATATTAGAACCAGCAGGTGCACTTGCACTAGCTGGAGCTGAGGCATACTGCAAGCATCATGGGGTCCAGGGGAAAG
upper sequence: AT3G10050.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0007g04310.t01 (Vitis vinifera), 3'ss of exon 4
-----------gtatggtacta-tccttgatacgttatcccttgtcagacggtgtttggcatatgcatactgaattgtagataatcagatacttgtctctacagGATATGTTTGAGGAGAAACGGAACATATTGGAACCAGCAGGGGCTCTTGCACTCGCTGGAGCTGAGGCATACTGTAAATATTATGGCCTAAAGGACGTGA
|| | | | | | | || ||| |||| || || || | | | | | || || ||| | | |||| | | | ||| | ||||||||||||||| ||| ||| || ||||| ||||| || ||||| || ||||||||||| || ||||| |||||||| ||| | |||| | |
gtaaatttgcttcattgaagaagtgatagctaagttgcaacttgacatttgg-gtgttgttgaggtctttggagtt--agaatttttggtactgatgt-tgcagAACATGTTTGAGGAGAAAAGGAGCATTTTAGAACCTGCAGGTGCGCTTGCCCTTGCTGGAGCTGAAGCGTACTGCAAATATTACGGCATCAAGGGAGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cggtgtttggcatatgcatactgaattgtagataatcagatacttgtctctacagGATATGTTTGAGGAGAAACGGAACATATTGGAACCAGCAGGGGCTCTTGCACTCGCTGGAGCTGAGGCATACTGTAAATATTATGGCCTAAAGGACGTGA
cttgtctct CT-rich tract
tagataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggtactatccttgatacgttatcccttgtcagacggtgtttggcatatgcatactgaattgtagataatcagatacttgtctctacagGATATGTTTGAGGAGAAACGGAACATATTGGAACCAGCAGGGGCTCTTGCACTCGCTGGAGCTGAGGCATACTGTAAATATTATGGCCTAAAGGACGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA