Sequence
atgc intronic sequence ATGC exonic sequence...tgtgtgccccccccaatatcatatggcatattaatccagtttttttttgtcttcatcatatagttgtttgttctaatgctttattttggttaattaacagGTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAG
Basic information
species | Glycine max |
transcript | GLYMA06G18170.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G18170.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g40740.1 (Oryza sativa), 3'ss of exon 6
---tgtgtgccccccccaatatcatatggcatattaatccagtttttttttgtcttcatcatatagttgttt-----gttctaatgctttattttggttaattaacagGTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAG
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gttagtggttttacattaaaatcagtcatca-actattctgctcccctcttttcaccttaatatttctgtattatgagcagtagtaaattgtgttctttttcctacagGTCCTCTATAAGCACAAGATCGTGCTATTTGGTGGTTTTTATGACACTCTTAGGGAAGTGAG
upper sequence: GLYMA06G18170.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G100815_T01 (Zea mays), 3'ss of exon 3
--tgtgtgccccccccaatatcatatggcatattaatccagtttttttttgtcttcatc-atatagttgtttgttctaatgctttattttggttaattaacagGTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAG
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aggacagacatatattcatttctt-tcccatgctcatattatacttctatattgccatctagccagtttaagacattctttatttatctttttt--tttgcagGTTCTTTACAAGCATAAGATTGTTCTATTTGGTGGCTTTTATGACACTCTTAGGGAAGTGAG
upper sequence: GLYMA06G18170.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 6
tgtgtgccccccccaatatcatatggcatattaatccagtttttttttgtcttcatcatatagttgtttgttctaatgctttattttggttaa--ttaacagGTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAG
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-gtggagttgtactactttcat-tatcaatctgttcctgccttcccttttgtaaccaactcatcaagttctcatcctgctctgctataatctactttttcagGTATTATACAAGCACAAGATCATAATTTTTGGTGGCTTCTATGATACTCTACGTGAAGTAAG
upper sequence: GLYMA06G18170.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g10130.t01 (Vitis vinifera), 3'ss of exon 6
-tgtgtgccccccccaatatcatatggcatattaatccagtttttttttgtcttcatcatatagttgtttgttctaatg-ctttattttggttaattaacagGTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAG
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ctgtat-tctataggaatgtatcataggtcatttattca-tcttatttgatattttgcactttttcactttttaaattaattttattttggacatgttacagGTTTTATACAAGCACAAGATTATTGTTTTTGGTGGCTTCTATGACACTCTCAGAGAAGTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtcttcatcatatagttgtttgttctaatgctttattttggttaattaacagGTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAG
tttattttggttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgtgccccccccaatatcatatggcatattaatccagtttttttttgtcttcatcatatagttgtttgttctaatgctttattttggttaattaacagGTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
tgtgtgc
- - - ccccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaatgc