Sequence
atgc intronic sequence ATGC exonic sequence...gcacagcctcaaggacagtaaaaatgctcttaactctccattttatcagccatgattgcggcagatcaattaatctgtagaaactttatcttgtgcacagTTTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTGTGTGAGCTTCACATTGTATTTAACTTCAACAAG
Basic information
| species | Oryza sativa |
| transcript | LOC_Os01g25110.1 |
| intron # | 4 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g25110.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G177914_T03 (Zea mays), 3'ss of exon 4
gcacagcctcaaggacagtaaaaatgctcttaactctccat--tttatcagccatgattgcggcagatcaattaatctgtagaaactttatcttgtgcacagTTTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTGTGTGAGCTTCACATTGTATTTAACTTCAACAAG
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--ataactgaagacttattttgtcttccttttgtctaaaaggacttatcagctctggttctaggagattgatcactctatactaactttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG
upper sequence: LOC_Os01g25110.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G177914_T05 (Zea mays), 3'ss of exon 4
gcacagcctcaaggacagtaaaaatgctcttaactctccat--tttatcagccatgattgcggcagatcaattaatctgtagaaactttatcttgtgcacagTTTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTGTGTGAGCTTCACATTGTATTTAACTTCAACAAG-----------------------------
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--ataactgaagacttattttgtcttccttttgtctaaaaggacttatcagctctggttctaggagattgatcactctatactaactttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGGTACCATATGTCCATATGATCCTACTTTT
upper sequence: LOC_Os01g25110.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G25400.1 (Glycine max), 3'ss of exon 5
-gcacagcctcaaggacagtaaaaat-gctcttaactctccattttatcagccatgattgcggcagatcaattaatctgtagaaactttatcttgtgcacagTTTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTGTGTGAGCTTCACATTGTATTTAACTTCAACAAG
|| | ||| | | | | | | | || || | | | | ||| ||| | | | || |||| ||||||||||||||||||| |||||||| ||||| ||||||||| | || || || |||| | |||
ggcttttgtgtagatgtgctaacagttgtttattgcagcctcttacatt-gttgttaattttatggattgatttgcttactttg-ttcctttctgccttcagTGTTTGTTGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG
upper sequence: LOC_Os01g25110.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S128_112V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------------------gcacagcctcaaggacagtaaaaatgctcttaactctccattttatcagccatgattgcggcagatcaattaatctgtagaaactttatcttg----tgcacagTTTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTGTGTGAGCTTCACATTGTATTTAACTTCAACAAG
| | ||| ||| ||| |||| ||||| | |||| || | || ||||| | ||| || | || | |||| ||||| || ||||||||| |||| ||||||||||| ||||||||| | || || | |||||| ||||
gtatgttttctgaagagagattctaattctaccttaccttgttatcctactagtactaaatgcatttgaagctaggatcagaggaaaagctattaatctatgatttttttagcccaaat--ctgcttgtcaatcttttcagcgaagtgttcttctggaactttgcagTGTTTGTAGAGACATTGGACCGATGTTTCAAGAATGTCTGTGAGCTTGATATAGTTTACAACTTCGGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagccatgattgcggcagatcaattaatctgtagaaactttatcttgtgcacagTTTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTGTGTGAGCTTCACATTGTATTTAACTTCAACAAG
aattaat putative branch site (score: 3)
ctttatctt putative PPT
atcaattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcacagcctcaaggacagtaaaaatgctcttaactctccattttatcagccatgattgcggcagatcaattaatctgtagaaactttatcttgtgcacagTTTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTGTGTGAGCTTCACATTGTATTTAACTTCAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
gcacagc
- - - - - - - - - - - aatgctc
- - - - - - - - - - - - - - - - - - - - - - - - gccatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcggca
