Sequence
atgc intronic sequence ATGC exonic sequence...tgtgatttcaccataggattgctaggcaaaactcctcctttttatattagtatagatatattttgaccacctccatccatatgcttcttctttgttctagACAGCTCTTCCTGCTCTTCCTGTCTTTCTCCTTGGCTGTTGAAGCACTACATGCATTTATGCAAGATGAGTCTGAGCATAA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g58580.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g58580.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G017365_T08 (Zea mays), 3'ss of exon 3
----tgtgatttcaccataggattgctaggcaaaactcctcctttttatattagtatagatatattttgaccacctccatccatatgcttcttctttgttctagACAGCTCTTCCTGCTCTTCCTGTCTTTCTCCTTGGCTGTTGAAGCACTACATGCATTTATGCAAGATGAGTCTGAGCATAA
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ggaaaaaaacaccctgtttgtattacacttttaaccctttctgtccttttgctttgtgctaacattttgaccaccacc----ctatggttcttta----tgtagacagCTGTTTCTATTGTTCCTGTCTTTCTCCTTGGCTGTTGAAGCATTACATGCATTTATGCAAGATGAATCGGAGCACAA
upper sequence: LOC_Os02g58580.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G017365_T09 (Zea mays), 3'ss of exon 2
--------tgtgatttcaccataggattgctaggcaaaactcctcctttttatattagtatagatatattttgaccacctccatccatatgcttcttctttgttctagACAGCTCTTCCTGCTCTTCCTGTCTTTCTCCTTGGCTGTTGAAGCACTACATGCATTTATGCAAGATGAGTCTGAGCATAA
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tgccggaaaaaaacaccctgtttgtattacacttttaaccctttctgtccttttgctttgtgctaacattttgaccaccacc----ctatggttcttta----tgtagACAGCTGTTTCTATTGTTCCTGTCTTTCTCCTTGGCTGTTGAAGCATTACATGCATTTATGCAAGATGAATCGGAGCACAA
upper sequence: LOC_Os02g58580.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G12100.1 (Arabidopsis thaliana), 3'ss of exon 3
tgtgatttcaccataggattgctaggcaaaactcctcctttttatattagtatagatatattttgaccacctccatccatatgcttctt--ctttgttctagACAGCTCTTCCTGCTCTTCCTGTCTTTCTCCTTGGCTGTTGAAGCACTACATGCATTTATGCAAGATGAGTCTGAGCATAA
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-----ccatacaatct-atcttttcgttttgcctttcattgtctctgtagtttatctttttggttaatactttgatttgtttaatatttgacatatgtgtagacagCTGTTCCTTATGTTCATGTCATTCTCCTTAGCTGTGGAAGCTCTTCATGCATTTATACAAGATGAATCAGAGCATAA
upper sequence: LOC_Os02g58580.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0007g06550.t01 (Vitis vinifera), 3'ss of exon 3
tgtgatttcaccataggattgctaggcaaaactcctcctttttatattagtatagatatattttgaccacctccatccatatgcttcttctttgt-tctagACAGCTCTTCCTGCTCTTCCTGTCTTTCTCCTTGGCTGTTGAAGCACTACATGCATTTATGCAAGATGAGTCTGAGCATAA
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-ttttcatcattatgtgattattgttgtcatcatttttcttgttggttgctgcctctagact---aacatgtaaatat-tttgattctgctgcatgtttagacagCTGTTTCTGTTGTTTATGTCATTCTCCTTGGCTGTGGAAGCACTTCATGCATTCATACAAGATGAATCTGAGCACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attagtatagatatattttgaccacctccatccatatgcttcttctttgttctagACAGCTCTTCCTGCTCTTCCTGTCTTTCTCCTTGGCTGTTGAAGCACTACATGCATTTATGCAAGATGAGTCTGAGCATAA
ttttgac putative branch site (score: 3)
tgcttcttctttgttc putative PPT
tatagatatattttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgatttcaccataggattgctaggcaaaactcctcctttttatattagtatagatatattttgaccacctccatccatatgcttcttctttgttctagACAGCTCTTCCTGCTCTTCCTGTCTTTCTCCTTGGCTGTTGAAGCACTACATGCATTTATGCAAGATGAGTCTGAGCATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG