Sequence
atgc intronic sequence ATGC exonic sequence...tttttgtatgtagtgtctactgtagttttgtgtttgtcttgtaaacagcataatatgtgatttcgttacaaccaaggtcttgactgatttcatcttgcagCCACACCCTGACGTCAAGCCGATGGCCTACGCGAACAACTTCCTCAGGATGTTCCAGTAACAACATATATCCATATCCGCCTTCTTTCGCCATATTTTTT
Basic information
species | Oryza sativa |
transcript | LOC_Os05g11550.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G126435_T02 (Zea mays), 3'ss of exon 11
----------------tttttgtatgtagtgtctactgtagtt--ttgtgtttgtcttgtaaacagcataatatgtgatttcgttacaaccaaggtcttgactgatttcatcttgcagCCACACCCTGACGTCAAGCCGATGGCCTACGCGAACAACTTCCTCAGGATGTTCCAGTAACAACATATATCCATATCCGCCTTCTTTCGCCATATTTTTT
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gttggctctttgaatatccttttatcatgttcctgttaaacttctttgcaccgatttgattagcaactggatatctgattgag--ggggtttacgctt--gctgGTGT-ATCTTGCAGCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATGTTTCAATGACGGAATATAACAACA------TTGTTTAGCAAT-------
upper sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G126435_T01 (Zea mays), 3'ss of exon 12
---tttttgtatgtagtgtctactgtagtt--ttgtgtttgtcttgtaaacagcataatatgtgatttcgttacaaccaaggtcttgactgatttcatcttgcagCCACACCCTGACGTCAAGCCGATGGCCTACGCGAACAACTTCCTCAGGATGTTCCAGTAACAACATATATCCATATC---CGCCTTCTTTCGCCATATTTTTT
| || ||| || || | | || ||| | | | | || | |||| ||||| | | | | ||| | | |||||||||||||| ||||| || ||||||||||| || || || ||||||||||||||||| || | || ||||| | | || | ||| || ||
atatccttttatcatgttcctgttaaacttctttgcaccgatttgattagcaactggatatctgattgag--ggggtttacgctt--gctggtgt-atcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATGTTTCAATGACGGAATATAACAACATTGTTTAGCAATTTTTATCAGATGA---
upper sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 12
tttttgtatgtagtgtctactgtagttttg-tgtttgtcttgtaaacagcataatatgtgattt-cgttacaaccaaggtcttgactgatttcatct----tgcagCCACACCCTGACGTCAAGCCGATGGCCTACGCGAACAACTTCCTCAGGATGTTCCAGTAACA-ACATATATCCATATCCGCCTTCTTTCGCCATATTTTTT
| | | ||| || | | | || | |||| || | | | |||| | || | || || | || | |||| | |||||||||||||||| ||||| || ||||| || || |||||||||||| |||||||| ||| | | | | || |||| |||| ||| ||
------aacaaattttctggtgcattatgactgcatatctttcaatctgtgttatatagggttgacattctttccttgtgtctggtttattttgttgaatatgcagCCACACCCTGATGTCAAACCTATGGCATATGCAAACAACTTCCTCCGGATGTTCTCATAATTTATACAGCTGACTAGAAGCCTAGAACTGCCA-ATTGTTA
upper sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA18G12440.1 (Glycine max), 3'ss of exon 12
-----------------------------------------------------------------------tttttgtatgtagtgtctactgtagttttgtgtttgtcttgtaaacagcata---atatgtgatttcgttacaaccaaggtct-tgactgatttcatct----tgcagCCACACCCTGACGTCAAGCCGATGGCCTACGCGAACAACTTCCTCAGGATGTTCCAGTAACAACATATATCCATATCCGCCTTCTTTCGCCATATTTTTT--
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tggttagtaccttttatgtttggagtatgctatgttatatcatgttttgtcatcctcaaaaaattaccaatatgttctttattgatttcatt-tatgaccgtgcatatctttcaatctgtattgttatatggggttgacatactttccttgtgtctggtttactttgttgaatatgcagcCACACCCTGATGTCAAACCTATGGCTTATGCAAACAACTTCCTCCGGATGTTCTCATAATT-TATACAGCTGACTAGAAGAAGCCCAGAACTGCCAATGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagcataatatgtgatttcgttacaaccaaggtcttgactgatttcatcttgcagCCACACCCTGACGTCAAGCCGATGGCCTACGCGAACAACTTCCTCAGGATGTTCCAGTAACAACATATATCCATATCCGCCTTCTTTCGCCATATTTTTT
gactgat putative branch site (score: 3)
tttcatctt CT-rich tract
taatatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttgtatgtagtgtctactgtagttttgtgtttgtcttgtaaacagcataatatgtgatttcgttacaaccaaggtcttgactgatttcatcttgcagCCACACCCTGACGTCAAGCCGATGGCCTACGCGAACAACTTCCTCAGGATGTTCCAGTAACAACATATATCCATATCCGCCTTCTTTCGCCATATTTTTT
- -ttgtatg
- - - - - - - -tctactg
- - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - -aacagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgactg