Sequence
atgc intronic sequence ATGC exonic sequencegtatcatgcatttttgaaaacatattttggtgcttcttttattttctttttcacccttgcatgccgtgactaaacagGGTGTTATTGAGTGCCCAAACCCGGATAAAGACATCCGAAGATTGGATGCAAACATACGGCTGTTTCCTCCATTTATTGATAACGACATTTGTCCATTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os11g25980.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g25980.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G411940_T01 (Zea mays), 3'ss of exon 7
------------------------------------------------------------gtatcatgcatttttgaaaacatattttggtgcttcttttattttctttttcacc-cttgcatgccgtgactaaacagGGTGTTATTGAGTGCCCAAACCCGGATAAAGACATCCGAAGATTGGATGCAAACATACGGCTGTTTCCTCCATTTATTGATAACGACATTTGTCCATTGA
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gttaaacttttatttgttttatctgcttcacttttgtttaatttttcttttgcggcagcagggtaacccccattttactatggattttagta-tgcattcatttaacttcccattacctttatgaattaactaaacagGGTGTGATCGAGTGCCCAATACCAGATAAAGACATACGAAGATTTGATGCAAACATCCGCCTGTTTCCTCCATTCATTGATAATGACATTTGCCCATTGA
upper sequence: LOC_Os11g25980.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G865163_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------------gtatcatgcatttttgaaaacatattttggtgcttcttttattttctttttcacc-cttgcatgccgtgactaaacagGGTGTTATTGAGTGCCCAAACCCGGATAAAGACATCCGAAGATTGGATGCAAACATACGGCTGTTTCCTCCATTTATTGATAACGACATTTGTCCATTGA
| | | | ||| | | ||||| || | | || |||| || || | | ||| | |||||||||||||| || |||||||||| || ||||||||||| |||||||| ||||||||||| || |||||||||||||| |||||||| |||||||| |||||||
gttaaacttttatttgttttatctgcttcacttttgttttaatttttcttttgcggcagcagggtaacccccattttactatggattttagta-tgcattcatttaacttcccattacctttatgaattaactaaacagGGTGTGATCGAGTGCCCAATACCAGATAAAGACATACGAAGATTTGATGCAAACATCCGCCTGTTTCCTCCATTCATTGATAATGACATTTGCCCATTGA
upper sequence: LOC_Os11g25980.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G33340.1 (Glycine max), 3'ss of exon 5
gtatcatgcatttttgaaaacatattttggtgcttcttttattttctttttcacccttgcatgccgtgactaaacagGGTGTTATTGAGTGCCCAAACCCGGATAAAGACATCCGAAGATTGGATGCAAACATACGGCTGTTTCCTCCATTTATTGATAACGACATTTGTCCATTGA-------------------------------------------------------------------------------------
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------------------------------------------------------------------------------gtgtaattgagtgtccctatccagataaagacatcaggagatttgatgcaaacatgcggctgtttcccccatttattgataatgatatatgccctttaaccattaaaaacaccattcttcagTCATGTTACTTGAGAAACACTGAGTGGGCATGTGGAGTGGCTGTGTATACAGGCAAGCCCAT
upper sequence: LOC_Os11g25980.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G37090.1 (Glycine max), 3'ss of exon 5
gtatcatgcatttttgaaaacatattttggtgcttcttttattttctttttcacccttgcatgccgtgactaaacagGGTGTTATTGAGTGCCCAAACCCGGATAAAGACATCCGAAGATTGGATGCAAACATACGGCTGTTTCCTCCATTTATTGATAACGACATTTGTCCATTGA
|| | | ||| | | || | | || | || ||| ||| | |||||||||||||||| || | || |||||||||||| | ||||| ||||||||||| ||||||||||| |||||||||||||| || || || || || |
------------gttaattatataggtcaactacttaatttctctattctctctgtgtgtatgt-gtgtgtctctagGGTGTTATTGAGTGTCCCTATCCAGATAAAGACATCAGGAGATTTGATGCAAACATGCGGCTGTTTCCCCCATTTATTGATAATGATATATGCCCTTTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattttggtgcttcttttattttctttttcacccttgcatgccgtgactaaacagGGTGTTATTGAGTGCCCAAACCCGGATAAAGACATCCGAAGATTGGATGCAAACATACGGCTGTTTCCTCCATTTATTGATAACGACATTTGTCCATTGA
ttcttttattttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcatgcatttttgaaaacatattttggtgcttcttttattttctttttcacccttgcatgccgtgactaaacagGGTGTTATTGAGTGCCCAAACCCGGATAAAGACATCCGAAGATTGGATGCAAACATACGGCTGTTTCCTCCATTTATTGATAACGACATTTGTCCATTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT