Sequence
atgc intronic sequence ATGC exonic sequencegtttgtcttcatgattattattattcttttgtagagcattgaagcggtaggaatcatacagtgtgtattcaccccgtctcctttatgtcttcagAGGTGTTTGCTGCAAGAGAGAAGAATGGTATATACATTCCAAGAGAACGCTACCTCCAAGAGGAAGCCGAGAAAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g02670.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g02670.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G024576_T01 (Zea mays), 3'ss of exon 7
gtttgtcttcatgattattattattcttttgtagagcattgaagcggtaggaatcatacagtgtgtattcaccccgtctcctttatgtcttcagAGGTGTTTGCTGCAAGAGAGAAGAATGGTATATACATTCCAAGAGAACGCTACCTCCAAGAGGAAGCCGAGAAAAAG
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-------------gttgttcttgcttttttttgtaac-tcggaatcataagaatcacacatcttgtattcatctggtctcctgtatatctccagAGGTGTTTGCTGCAAGAGAGAAGAACGGTATCTATATTCCAAGAGAGCGCTACCTCCAAGAAGAAGCTGAGAAAAAG
upper sequence: LOC_Os05g02670.3 (Oryza sativa), 3'ss of exon 8
lower sequence: AT3G45850.1 (Arabidopsis thaliana), 3'ss of exon 8
gtttgtcttcatgattattattattcttttgtagagcattgaagcggtaggaatcatacagtgtgtattcaccccgtctcctttatgtcttcagAGGTGTTTGCTGCAAGAGAGAAGAATGGTATATACATTCCAAGAGAACGCTACCTCCAAGAGGAAGCCGAGAAAAAG
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----------------------gtaacagtat-gatcattttatc--cattagtttcaaggcattccttaataac-tttcctctattttcttagAGGTATATGCTGCAAGAGAGAAGAATGGGATTTATATTCCAAAAGACCGCTACATTCAAGAAGAGGCTGAGAAAAAG
upper sequence: LOC_Os05g02670.3 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv06s0004g03810.t01 (Vitis vinifera), 3'ss of exon 8
----------------------------------gtttgtcttcatgattattattattctt-ttgtagagcattgaagcggtaggaatcatacagtgtgtattcaccccgtctcctttatgtct--tcagAGGTGTTTGCTGCAAGAGAGAAGAATGGTATATACATTCCAAGAGAACGCTACCTCCAAGAGGAAGCCGAGAAAAAG
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gttgttaatgctttttatatataatcttatgcatggtcagatagatgaatcatatagttattattattagacaattgagtggtaaaga--gtaaattatgcaa-catcttgatgtttttatctttaatcagAGGTCTATGCTGCAAGAGAGAAGAATGGTATCTATATACCTCGAGATCGTTATCTTAATGAAGAAGCAGAGAAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaagcggtaggaatcatacagtgtgtattcaccccgtctcctttatgtcttcagAGGTGTTTGCTGCAAGAGAGAAGAATGGTATATACATTCCAAGAGAACGCTACCTCCAAGAGGAAGCCGAGAAAAAG
ccccgtctcctttatg CT-rich tract
aatcata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtcttcatgattattattattcttttgtagagcattgaagcggtaggaatcatacagtgtgtattcaccccgtctcctttatgtcttcagAGGTGTTTGCTGCAAGAGAGAAGAATGGTATATACATTCCAAGAGAACGCTACCTCCAAGAGGAAGCCGAGAAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA