Sequence
atgc intronic sequence ATGC exonic sequence...gattggtcggtgtattacaaattatgtctaggtttctactgtttcattgtcttgggttgttttcttcgattgaagattaatgatctaaaatggtttgcagCTTAGGTTTTTAAAACGGATCAAATAGTATTCTTTGTCGGGCGGATATTTCAAGGCCTACTCCGGAAGGAATGCCCTTGTGCAACAGGCAAAAAAAAGTG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g48960.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g48960.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G020928_T02 (Zea mays), 3'ss of exon 1
gattggtcggtgtattacaaattatgtctaggtttctactgtttcattgtcttgggttgttttcttcg-----attgaagattaatgatctaaaatggtttgcagCTTAGGTTTTTAAAACGGATCAAATAGTATTCTTTGTCGGGCGGATATTTCAAGGCCTACTCCGGAAGGAATGCCCTT-GTGCAACAGGCAAAAAAAAGTG----------
|| ||| || | || ||| || | | | || |||||||| |||| || | |||||| |||||||||||| ||||||||||| |||||| | |||| |||||||||||||| | |||||||||| || ||||||| ||||| |||| |||||| || | ||
---ctactaatggattttgccttct--cttggtggtagctttaactgcgatttcggttgtttgtttcgtttctatcagatattaataatctaaaatggtgtgcagCTTAGG---TTAAAATCAAAAAAAT--------TTGTCGGGCGGATAATACAAGGCCTACACCAGAAGGAACACCCTTTGTGCGACAGGCGAACAGCTGTCTCTATCTCTC
upper sequence: LOC_Os05g48960.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G025014_T01 (Zea mays), 3'ss of exon 1
-gattggtcggtgtattacaaattatgtctaggtttctactgtttcattgtcttgggttgtttt-cttcgattgaagattaatgatctaaaatggtttgcagCTTAGGTTTTTAAAACGGATCAAATAGTATTCTTTGTCGGGCGGATATTTCAAGGCCTACTCCGGAAGGAATGCCCTT-GTGCAACAGGCAAAAAAAAGTG
| | | | ||| | || | || |||| ||| | | |||||| ||| || | |||||| |||||||||||| ||||||||||| |||||| | |||| |||||||||||||| | |||||||||| || |||||||| ||||| |||| |||||| || |
ctactaatggatgttgccttttcttggtggtagctttaactgcg--atttcggttgtttgtttcgtttctatcagatattaataatctaaaatggtgtgcagCTTAGG---TTAAAATCAAAAAAAT--------TTGTCGGGCGGATAATACAAGGCCTACACCAGAAGGAATACCCTTTGTGCGACAGGCGAACAGCT---
upper sequence: LOC_Os05g48960.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G025014_T01 (Zea mays), 3'ss of exon 1
-gattggtcggtgtattacaaattatgtctaggtttctactgtttcattgtcttgggttgtttt-cttcgattgaagattaatgatctaaaatggtttgcagCTTAGGTTTTTAAAACGGATCAAATAGTATTCTTTGTCGGGCGGATATTTCAAGGCCTACTCCGGAAGGAATGCCCTT-GTGCAACAGGCAAAAAAAAGTG
| | | | ||| | || | || |||| ||| | | |||||| ||| || | |||||| |||||||||||| ||||||||||| |||||| | |||| |||||||||||||| | |||||||||| || |||||||| ||||| |||| |||||| || |
ctactaatggatgttgccttttcttggtggtagctttaactgcg--atttcggttgtttgtttcgtttctatcagatattaataatctaaaatggtgtgcagCTTAGG---TTAAAATCAAAAAAAT--------TTGTCGGGCGGATAATACAAGGCCTACACCAGAAGGAATACCCTTTGTGCGACAGGCGAACAGCT---
upper sequence: LOC_Os05g48960.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G025014_T04 (Zea mays), 3'ss of exon 1
-gattggtcggtgtattacaaattatgtctaggtttctactgtttcattgtcttgggttgtttt-cttcgattgaagattaatgatctaaaatggtttgcagCTTAGGTTTTTAAAACGGATCAAATAGTATTCTTTGTCGGGCGGATATTTCAAGGCCTACTCCGGAAGGAATGCCCTT-GTGCAACAGGCAAAAAAAAGTG----------
| | | | ||| | || | || |||| ||| | | |||||| ||| || | |||||| |||||||||||| ||||||||||| |||||| | |||| |||||||||||||| | |||||||||| || |||||||| ||||| |||| |||||| || | ||
ctactaatggatgttgccttttcttggtggtagctttaactgcg--atttcggttgtttgtttcgtttctatcagatattaataatctaaaatggtgtgcagCTTAGG---TTAAAATCAAAAAAAT--------TTGTCGGGCGGATAATACAAGGCCTACACCAGAAGGAATACCCTTTGTGCGACAGGCGAACAGCTGTCTCTCTCTCTG
upper sequence: LOC_Os05g48960.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G025014_T04 (Zea mays), 3'ss of exon 1
-gattggtcggtgtattacaaattatgtctaggtttctactgtttcattgtcttgggttgtttt-cttcgattgaagattaatgatctaaaatggtttgcagCTTAGGTTTTTAAAACGGATCAAATAGTATTCTTTGTCGGGCGGATATTTCAAGGCCTACTCCGGAAGGAATGCCCTT-GTGCAACAGGCAAAAAAAAGTG----------
| | | | ||| | || | || |||| ||| | | |||||| ||| || | |||||| |||||||||||| ||||||||||| |||||| | |||| |||||||||||||| | |||||||||| || |||||||| ||||| |||| |||||| || | ||
ctactaatggatgttgccttttcttggtggtagctttaactgcg--atttcggttgtttgtttcgtttctatcagatattaataatctaaaatggtgtgcagCTTAGG---TTAAAATCAAAAAAAT--------TTGTCGGGCGGATAATACAAGGCCTACACCAGAAGGAATACCCTTTGTGCGACAGGCGAACAGCTGTCTCTCTCTCTG
upper sequence: LOC_Os05g48960.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G020928_T03 (Zea mays), 3'ss of exon 1
gattggtcggtgtattacaaattatgtctaggtttctactgtttcattgtcttgggttgttttcttcg-----attgaagattaatgatctaaaatggtttgcagCTTAGGTTTTTAAAACGGATCAAATAGTATTCTTTGTCGGGCGGATATTTCAAGGCCTACTCCGGAAGGAATGCCCTT-GTGCAACAGGCAAAAAAAAGTG
|| ||| || | || ||| || | | | || |||||||| |||| || | |||||| |||||||||||| ||||||||||| |||||| | |||| |||||||||||||| | |||||||||| || ||||||| ||||| |||| |||||| || |
---ctactaatggattttgccttct--cttggtggtagctttaactgcgatttcggttgtttgtttcgtttctatcagatattaataatctaaaatggtgtgcagCTTAGG---TTAAAATCAAAAAAAT--------TTGTCGGGCGGATAATACAAGGCCTACACCAGAAGGAACACCCTTTGTGCGACAGGCGAACAGCT---Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|29685226|gb|CB681501.1|CB681501EST: AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAG CTTAGGTTTTTAAAACGGATCAAATAGTATTCTTTGTCGGGCGGATATTTC
genomic: AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAGgttcgtgttc ... tggtttgcagCTTAGGTTTTTAAAACGGATCAAATAGTATTCTTTGTCGGGCGGATATTTC
EST:
gi|29633920|gb|CB638929.1|CB638929EST: AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAG CTTAGGTTTTTAAAACGGATCAAATAGTATTCTTTGTCGGGCGGATATTTC
genomic: AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAGgttcgtgttc ... tggtttgcagCTTAGGTTTTTAAAACGGATCAAATAGTATTCTTTGTCGGGCGGATATTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgtcttgggttgttttcttcgattgaagattaatgatctaaaatggtttgcagCTTAGGTTTTTAAAACGGATCAAATAGTATTCTTTGTCGGGCGGATATTTCAAGGCCTACTCCGGAAGGAATGCCCTTGTGCAACAGGCAAAAAAAAGTG
atctaaa putative branch site (score: 3)
attaatgatctaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gattggtcggtgtattacaaattatgtctaggtttctactgtttcattgtcttgggttgttttcttcgattgaagattaatgatctaaaatggtttgcagCTTAGGTTTTTAAAACGGATCAAATAGTATTCTTTGTCGGGCGGATATTTCAAGGCCTACTCCGGAAGGAATGCCCTTGTGCAACAGGCAAAAAAAAGTG
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