Sequence
atgc intronic sequence ATGC exonic sequence...gtttaattcatttcgtattgtttttttccttgcataaatctaagatatgcatgcatatattgtttgtttatactatctgaagcagtgaatgtgttgacagGTTTGGTGCATGCTTTTGAATGACAAAGTTCAGTTCAGGATGCAGTGGCCCCAATATGCAGAATTGCATGTTAATG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g03430.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g03430.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G455664_T01 (Zea mays), 3'ss of exon 8
--gtttaattcatttcgtattgtttttttccttgcataaatctaagatatgcatgcatatattgtttgtttatactatctgaagcagtgaatgtgttgacagGTTTGGTGCATGCTTTTGAATGACAAAGTTCAGTTCAGGATGCAGTGGCCCCAATATGCAGAATTGCATGTTAATG
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tctcatgtcctatccagcaaagaaaaagcacttggataca-ctcactcgttctgttgcacagtcctgttaactaccggttgt-gttgtgggtctgtggacagGTTTGGTGCATTCTTGTAAATGACAAAGTCCAGTTCAGGATGCAATGGCCTCAATATGCAGAATTGCAAGTGAACG
upper sequence: LOC_Os05g03430.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G155123_T03 (Zea mays), 3'ss of exon 8
gtttaattcatttcgtattgtttttttccttgcataaatctaagatatgcatgcatatattgtt---tgtttatactatctg------aagcagtgaatgtgttgacagGTTTGGTGCATGCTTTTGAATGACAAAGTTCAGTTCAGGATGCAGTGGCCCCAATATGCAGAATTGCATGTTAATG
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---------ttatcatgtcctattcaacaaagaaaaacacttggatacactcactggttctgttgcacagtcctgttaactaccgattgtgttgtgggtctgtggacagGTTTGGTGCATCCTTATAAATGACAAAGTCCAGTTCAGGATGCAATGGCCTCAATATGCAGAATTGCAAGTGAACG
upper sequence: LOC_Os05g03430.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G40320.1 (Glycine max), 3'ss of exon 5
gtttaattcatttcgtattgtttttttccttgcataaatctaagatatgcatgcatatattgtttgtttatacta-tctgaagcagtgaatgtgttgacagGTTTGGTGCATGCTTTTGAATGACAAAGTTCAGTTCAGGATGCAGTGGCCCCAATATGCAGAATTGCATGTTAATG
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----------------------gttggtttggtttagtgctagtagtttaatgcata-attctatcctggtaataatgtatggcaattgtttcatatctagGTTTGGTGTATGCTTTTGAATGACAAGGTTTCATTCAGGATGCAATGGCCACAGTTTGCAGATCTAAAGGTCAATG
upper sequence: LOC_Os05g03430.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA12G29270.1 (Glycine max), 3'ss of exon 5
gtttaattcatttcgtattgtttttttccttgcataaatctaagatatgcatgcatatattgtttgttta--tactatctgaagcagtgaatgtgttgacagGTTTGGTGCATGCTTTTGAATGACAAAGTTCAGTTCAGGATGCAGTGGCCCCAATATGCAGAATTGCATGTTAATG
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----------------------gttggtttggtttagtgctagtagtttgatgcata-actttctatccaggtattaatgtatgccaattgtttcatattagGTTTGGTGTATGCTTTTGAATGACAAGGTTTCATTCAGGATGCAATGGCCACAATTTGCAGATCTAAAGGTCAATG
upper sequence: LOC_Os05g03430.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G60410.5 (Arabidopsis thaliana), 3'ss of exon 9
gtttaattcatttcgtattgtttttttccttgcataaatctaagatatgcatgcatatattgtttgtttatactatctgaagcagtgaatgtgttgacagGTTTGGTGCATGCTTTTGAATGACAAAGTTCAGTTCAGGATGCAGTGGCCCCAATATGCAGAATTGCATGTTAATG
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---------gttgggttttgtaaactacatttaatatgtc-aaggtgtatctacctatac-----gttt---ctaactggaa-atcaattttgtt--tagGCTTGGTGTATGCTCTTGAATGATAAAGTTCTCTTTAGGATGCAGTGGCCTCAGTATGCTGATCTGCAGGTCAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgcatgcatatattgtttgtttatactatctgaagcagtgaatgtgttgacagGTTTGGTGCATGCTTTTGAATGACAAAGTTCAGTTCAGGATGCAGTGGCCCCAATATGCAGAATTGCATGTTAATG
atatattgtttgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttaattcatttcgtattgtttttttccttgcataaatctaagatatgcatgcatatattgtttgtttatactatctgaagcagtgaatgtgttgacagGTTTGGTGCATGCTTTTGAATGACAAAGTTCAGTTCAGGATGCAGTGGCCCCAATATGCAGAATTGCATGTTAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG