Sequence
atgc intronic sequence ATGC exonic sequence...cctgtaacacgtacaacttatcgccttttgaaagtatactgagacatcttcctgcaatattttgcctgctcataatctgacaacaatattttgtttgtagTTAAAGCGGAAACATGACAGAGAAGAGAATGAAGCTGCTGAATCAAATGACTGGATGATGAGCCCTGGATACACTAATCCAGCAGGCAGCCCAGTTCCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os12g06200.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g06200.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G052515_T01 (Zea mays), 3'ss of exon 1
cctgtaacacgtacaacttatcgccttttgaaagtat---actgagacatcttcctgcaatattttgcct-gctcataatctgacaacaatattttgtttgtagTTAAAGCGGAAACAT---GACAGAGAAGAGAATGAAGCTGCTGAATCAAATGACTGGATGATGAGCCCTGGATACACTAATCCAGCAGGCAGCCCAGTTCCAA
|| || | || | |||||| |||| || || ||| | | || | || | |||| | ||| |||| || || ||| |||| || ||||||||| |||||| ||| ||||||||||| ||||||||||||||||| |||||||||||| ||||| | | ||||||||||||| |
----caaatattatatctcaaatccttttcaaagcattacgctttaccatttgcatgtgactccttatttagctccgattctaacaagaaccttcctattgcagTTGAAACGGAAACATAACGACAGAACAGAAAATGAAGCTGCCGAATCAAATGACTGGAT---GAGCCCTGGATATGCTAATGCTGGCAGCAGCCCAGTTCCTA
upper sequence: LOC_Os12g06200.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G086401_T01 (Zea mays), 3'ss of exon 4
------------------------------cctgtaacacgtacaacttatcgccttttgaaagtatactgaga---catcttcctgcaatattttgcct-gctcataatctgacaacaatattttgtttgtagTTAAAGCGGAAACAT---GACAGAGAAGAGAATGAAGCTGCTGAATCAAATGACTGGATGATGAGCCCTGGATACACTAATCCAGCAGGCAGCCCAGTTCCAA-------------------------------------
| || || | || | |||||| |||| || | | ||||| | || | || | |||| | ||| |||| || || ||| |||| || ||||||||| |||| | | | ||||||||||| ||||||||||||||||| |||||||||||| ||||| | | ||||||||||||| |
gtaaccatgtgggtggtcttagtgatgctgctcacaaatattatatctcaaatccttttcaaagcattacgcgttaccatctgcatgtgactccttatttagctccgattctaacaagaaccttcctattgcagttgaaacggaaacataacgacataacataaaatgaagCTGCCGAATCAAATGACTGGAT---GAGCCCTGGATATGCTAATGCTGGCAGCAGCCCAGTTCCTACACCCCCTTCAGGGAAAGGTTTGAAAGCATCCACCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcttcctgcaatattttgcctgctcataatctgacaacaatattttgtttgtagTTAAAGCGGAAACATGACAGAGAAGAGAATGAAGCTGCTGAATCAAATGACTGGATGATGAGCCCTGGATACACTAATCCAGCAGGCAGCCCAGTTCCAA
atctgac putative branch site (score: 3)
ttttgttt putative PPT
aacaatattttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctgtaacacgtacaacttatcgccttttgaaagtatactgagacatcttcctgcaatattttgcctgctcataatctgacaacaatattttgtttgtagTTAAAGCGGAAACATGACAGAGAAGAGAATGAAGCTGCTGAATCAAATGACTGGATGATGAGCCCTGGATACACTAATCCAGCAGGCAGCCCAGTTCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacaat