Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttgttgctgctagtacattccactcaaaacaccttttgtttctgctgattttgcattgcttttcacttccttcctcctgtgaactcggatgctttctgatcaaaatttactactttctgaagctttgctgatgtctgtaactaccgagagaattctaactttggcatgatttattctatcagGAAGGTGATCCTCGGCTGTCAAGTTTTGGACTAATGAAGAACAGCCGCGATGGGAAAAGTTATAGCACTAATCTGGCTTACACCCCGCCTGAGTTTCTAC
Basic information
| species | Oryza sativa |
| transcript | LOC_Os10g42110.1 |
| intron # | 4 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g42110.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G054634_T02 (Zea mays), 3'ss of exon 4
gtatgtttgttgctgctagtacattccactcaaaacaccttttgtttctgctgattttgcattgcttttcacttccttcctcctgtgaactcggatgctttctgatcaaaatttactactttctgaagctttgctgatgtctgtaactaccgagagaattctaactttggcatgatttatt--------ctatcagGAAGGTGATCCTCGGCTGTCAAGTTTTGGACTAATGAAGAACAGCCGCGATGGGAAAAGTTATAGCACTAATCTGGCTTACACCCCGCCTGAGTTTCTAC
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----------------------------------------------------------------------------------------atatgaag--ttgccaat-gtgatttttcacctgttataatt-----gattatcttagctgcctaaagaatacctcacctgttgtaatcaatttctattccctatcagGAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGATGGGAAAAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTAC
upper sequence: LOC_Os10g42110.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G169080_T01 (Zea mays), 3'ss of exon 4
gtatgtttgttgctgctagtacattccactcaaaacaccttttgtttctgctgattttgcattgcttttcacttccttcctcctgtgaactcggatgctttctgatcaaaatttactactttctgaagctttgctgatgtctgtaactaccgagagaattctaactttggcatgatttatt--------ctatcagGAAGGTGATCCTCGGCTGTCAAGTTTTGGACTAATGAAGAACAGCCGCGATGGGAAAAGTTATAGCACTAATCTGGCTTACACCCCGCCTGAGTTTCTAC
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-----------------------------------------------------------------------------------------atctgtagttgccta--tgtggttttttacctgttgtaatt-----gattattgtagctgcctaaggaatacatcgcctgttgtaaccgatttctattccctatcagGAAGGTGATCCCCGCCTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGATGGAAAAAGCTATAGTACTAACCTGGCTTACACTCCACCAGAGTTTCTAC
upper sequence: LOC_Os10g42110.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatgtttgttgctgctagtacattccactcaaaacaccttttgtttctgctgattttgcattgcttttcacttccttcctcctgtgaactcggatgctttctgatcaaaatttactactttctgaagctttgctgatgtctgtaactaccgagagaattctaactttggcatgatttattctatcagGAAGGTGATCCTCGGCTGTCAAGTTTTGGACTAATGAAGAACAGCCGCGATGGGAAAAGTTATAGCACTAATCTGGCTTACACCCCGCCTGAGTTTCTAC
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--------------------------------------------------------------------------------ttttgtggttt----ttcctttgaactagctctgcttggtatgtggatgttaactaaagtctagaaa-acggttag---tttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
upper sequence: LOC_Os10g42110.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S122_66V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatgtttgttgctgctagtacattccactcaaaacaccttttgtttctgctgattttgcattgcttttcacttccttcctcctgtgaactcggatgct-----ttctgatcaaaatttactactttctg-aagctttgctgatgtctgtaactaccgagagaattctaactttggcatgatttat---tctatcagGAAGGTGATCCTCGGCTGTCAAGTTTTGGACTAATGAAGAACAGCCGCGATGGGAAAAGTTATAGCACTAATCTGGCTTACACCCCGCCTGAGTTTCTAC
|||| | || ||| | || | ||||| | ||| || | || | | || | | || |||| | | || |||| ||| ||| ||| ||| | || ||| | ||| ||| || | | | | ||||||||| ||||| || || || ||||||| || ||||||||||| |||||||| ||||| ||||| || |||||||| ||||| || ||||| | ||
gtattgctcttctctgtagcagttttgaactaaaacttggtatgtcccttcccgttcctatcaagtctcgacaatcctgctatacagaacacccacatcaaatacgctaatcacttttttttacggaaaataaggttttaaagtagacctatctaatctgtagattataaattgatggtctcccacgcctttgtcagGAAGGAGATCCGCGCCTCTCTTGTTTTGGCCTCATGAAGAACAGTCGCGATGGAAAAAGCTATAGTACCAATCTGGCCTACACTCCCCCTGAATACTTAA
upper sequence: LOC_Os10g42110.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S9_348V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatgtttgttgctgctagtacattccactcaaaacaccttttgtttctgctgattttgcattgcttttcacttccttcctcctgtgaactcggatgctttctgatcaaaatttactactttctgaagctttgctgatgtctgta-actaccgagagaattctaactttggcatgatttattctatcagGAAGGTGATCCTCGGCTGTCAAGTTTTGGACTAATGAAGAACAGCCGCGATGGGAAAAGTTATAGCACTAATCTGGCTTACACCCCGCCTGAGTTTCTAC
|| |||| | | |||| | | | || | || | | ||| || || | | | || ||| || | ||||| | |||| || || || || || || ||||||| || |||||||||||| | ||||| ||||| || ||||| ||| |||||||||| || ||||||| |
--------------------------------------------------------------------------------tcgtgtgggtt----tcctttggaaatagttctacttagtacgtggatttcaactgcagttaatagaatgctcagtatattaacgattctctacgattttgt-----agGACGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGAAAAAGCTACAGCACCAATTTGGCTTACACTCCTCCTGAGTACTTGAMapped 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|58678612|gb|CK067299.1|CK067299EST: ACCGAAAAATCTATCATGACTTGAATGCTTATAGAGTACTTTTTGATGAG GAAGGTGATCCTCGGCTGTCAAGTTTTGGACTAATGAAGAACAGCCGCGAT
genomic: ACCGAAAAATCTATCATGACTTGAATGCTTATAGAGTACTTTTTGATGAGgtatgtttgt ... attctatcagGAAGGTGATCCTCGGCTGTCAAGTTTTGGACTAATGAAGAACAGCCGCGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgatgtctgtaactaccgagagaattctaactttggcatgatttattctatcagGAAGGTGATCCTCGGCTGTCAAGTTTTGGACTAATGAAGAACAGCCGCGATGGGAAAAGTTATAGCACTAATCTGGCTTACACCCCGCCTGAGTTTCTAC
ttctaac putative branch site (score: 1)
tttattct putative PPT
atgatttattctat TA-rich tract
