Sequence
atgc intronic sequence ATGC exonic sequencegtgaatgatataaaggcaagcaattttatttttcttgattaactgactacaagttatttgcggtttcgcgtgatttcatcttagtaagattttcactaacacaacacttgggagatatgtactttcatttttctggaagactaatatggttcaaatccctgttatgcagAGAGCAGTAGCATCGGCAAACAAAAGAACCACAGTCCGTTTTAAAGAGTTGAACCAAAAGAAATACCGCACTCCCTTACTG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g49260.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g49260.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G077546_T02 (Zea mays), 3'ss of exon 8
gtgaatgatataaaggcaagcaattttatttttcttgatta-actgactacaagttatttgcggtttcgcgtgatttcatcttagtaagattttcactaacacaacacttgggagatatgtactttcattt--ttctggaagactaatatggttcaaatccctgtt--atgcagAGAGCAGTAGCATCGGCAAACAAAAGAACCACAGTCCGTTTTAAAGAGTTGAACCAAAAGAAATACCGCACTCCCTTACTG
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---------------gcgtgcactttactttcattcatttagactgattgaatactgttta----tttgaatagtcttcactttgtgtattattatctt---taacatttggcatatgtctctatgtacttcattctgatgaaatcagttggatccacttttagctctatgcagATAGCTGTGACATCAGCAAACAAAAGTGGTACAATAAGTTTTCAAGAGTTGAACCAAAAGAAAAACCGCACGCCCCTAATT
upper sequence: LOC_Os05g49260.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G160430_T04 (Zea mays), 3'ss of exon 8
gtgaatgatataaaggcaagcaattttatttttcttgattaactgactacaagttatttgcggtttcgcgtgatttcatcttagtaagattttcactaacacaacac-ttgggagatatgtactttcatttttctggaagactaatatggttcaaatccctgttatgcagAGAGCAGTAGCATCGGCAAACAAAAGAACCACAGTCCGTTTTAAAGAGTTGAACCAAAAGAAATACCGCACTCCCTTACTG
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-----------gtaagcacttactttcattcatctataatgactgcgtgcagtttatttgaacagtcttcacttcctgtcttatta---ttttctttaacctttcgtgcctggatctatgtactt-cattcttgtggaa--------------------tctttatgcagATAGCTGTAGCATCAGCAAACAAAAGTGGTACAATAAGCTTTCGAGAGTTGAACCAAAAGAAATACCGCACGCCTCTAATT
upper sequence: LOC_Os05g49260.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G160460_T02 (Zea mays), 3'ss of exon 8
gtgaatgatataaaggcaagcaattttattt-ttctt-gattaactgactacaagttatttg--cggtttcgcgtgatttcatcttagtaagattttcactaacacaacacttgggagatatgtactttcatttt-tctggaagactaa---tatggttcaaatccctgttatgcagAGAGCAGTAGCATCGGCAAACAAAAGAACCACAGTCCGTTTTAAAGAGTTGAACCAAAAGAAATACCGCACTCCCTTACTG
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---------------gttagcacttccctttgttcttagactgactgaatatgatttatgtgatcaatcttccctttgggtatctttatttctttaacattgaacacatgtttatatgtaattcatttttatgaaatcagtgggattaactctttaggtttggtccccattatgcagAGAGCAGTAATGTCAGCAAACAAAAGGGCTACAATTCGTTTCCAAGAGTTGAACCAAAAGAAATACCGAACGCCCCTAATT
upper sequence: LOC_Os05g49260.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G098679_T03 (Zea mays), 3'ss of exon 8
gtgaatgatataaaggcaagcaattttatttttcttgattaactgactacaagttatttgcggtttcgcgtgatttcatcttagtaagattttcactaacacaacacttgggagat------atgtactttcatttttctggaagactaatatggttcaaatccctg---ttatgcagAGAGCAGTAGCATCGGCAAACAAAAGAACCACAGTCCGTTTTAAAGAGTTGAACCAAAAGAAATACCGCACTCCCTTACTG
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-----------gcacgcacctgcttccactcatctagaatggatggatacagcttatttgaaaacagtcttcactctgtatcattactactatttcc--ttcaacatttggtgcatggctccatgtgctt-cattcttgtggaatcggaggtgggatcaactttttaattttatgcagATAGCTGTAGCATCGGCAAACAAAAGTGGTGCAATGAGCTTTCAAGAGTTGAACCAGAAGAAATACCGCACGCCCCTAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatgtactttcatttttctggaagactaatatggttcaaatccctgttatgcagAGAGCAGTAGCATCGGCAAACAAAAGAACCACAGTCCGTTTTAAAGAGTTGAACCAAAAGAAATACCGCACTCCCTTACTG
gactaat putative branch site (score: 2)
tccctgtt putative PPT
tttcattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaatgatataaaggcaagcaattttatttttcttgattaactgactacaagttatttgcggtttcgcgtgatttcatcttagtaagattttcactaacacaacacttgggagatatgtactttcatttttctggaagactaatatggttcaaatccctgttatgcagAGAGCAGTAGCATCGGCAAACAAAAGAACCACAGTCCGTTTTAAAGAGTTGAACCAAAAGAAATACCGCACTCCCTTACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA