Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttagtattcagtatttcagttccttgtgccctttgttctacgaattcatagcttgctaccaagactgtaaagctactatttgttctttgtgaccattgcaaagtctaaagttttaaccctgtctgttcttcttactgaacagGAAATTCCAGATAACGAGTTTGAGAAGCGCATCAGGCCAGAGGTTATACCAGCCAGTGAGATAGGAGTGACTTTTGATGACATTGGAGCCCTGGCTGACA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g50750.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g50750.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G128748_T01 (Zea mays), 3'ss of exon 11
gtaagtttagtattcagtatttcagttccttgtgccctttgttctacgaattcatagcttgctaccaagactgtaaagctactatttgttctttgtgaccattgcaaagtctaaagttttaaccctgtctg--ttcttcttactgaacagGAAATTCCAGATAACGAGTTTGAGAAGCGCATCAGGCCAGAGGTTATACCAGCCAGTGAGATAGGAGTGACTTTTGATGACATTGGAGCCCTGGCTGACA
|||| | || ||| | || || || || | ||| | | | || | || ||| |||||| ||||||| || |||||||| ||||| ||||| |||||||| || || || ||||||||||||||||| || |||||||| ||||||||||| || |
------------------------------------------------------------------------gtaa-gtcgtcatcagttgactctgccccctgt---gttcttttcctcaacgttaacagcatttgtgtttttgagcagGAAGTTCCAGACAATGAGTTTGAAAAGCGTATCAGACCAGAGGTCATTCCGGCAAGTGAGATAGGAGTGACATTCGATGACATCGGAGCCCTGGCAGATA
upper sequence: LOC_Os05g50750.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA09G23250.1 (Glycine max), 3'ss of exon 10
gtaagtttagtattcagtatttcagttccttgtgccctttgttctacgaattcatagct-tgctaccaagactgtaaagctactatttgttctttgtgaccattgcaaagtctaaagttttaaccctgtctgttcttcttactgaacagGAAATTCCAGATAACGAGTTTGAGAAGCGCATCAGGCCAGAGGTTATACCAGCCAGTGAGATAGGAGTGACTTTTGATGACATTGGAGCCCTGGCTGACA
| | | | |||| || | | | | |||| || | | || || || || | | ||| || | | | ||| || |||||| |||| || |||||||||||||||||||| || ||||||||||| || || | ||||||||| || || |||| || ||||| || ||| ||| |
---------------------------------------ctagccatgtaactgaagctgtgtgatataaattctaaacttatttccttttactttgccccctt------ttttgtgtt---actatatactaattgcttgcttg-cagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCGTTGGATGAGA
upper sequence: LOC_Os05g50750.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA16G29040.1 (Glycine max), 3'ss of exon 10
gtaagtttagtattcagtatttcagttccttgtgccctttgttctacgaattcatagcttgctaccaagactgtaaagctactatttgttctttgtgaccattgcaaagtctaaagttttaaccctgtctgttcttcttactgaacagGAAATTCCAGATAACGAGTTTGAGAAGCGCATCAGGCCAGAGGTTATACCAGCCAGTGAGATAGGAGTGACTTTTGATGACATTGGAGCCCTGGCTGACA
||| || || ||| | || | |||| | || || | | || | | | | ||| || | | ||||| || |||||| |||| || |||||||||||||||||||| || ||||||||||| || || | ||||||||| || || |||| || ||||| || ||| ||| |
------------------------------------------actagccatgcagctgaagctgt-atgatt-taaattctaaacttatttccttttactttcccccttttttgtgtt---actatatactaatttcttgcttg-cagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCATTGGATGAGA
upper sequence: LOC_Os05g50750.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA05G37290.1 (Glycine max), 3'ss of exon 12
gtaagtttagtattcagtatttcagttccttgtgccctttgt-tctacgaattcatagcttgctaccaagactgtaaagctactatttgttctttgtgaccattgcaaagtctaaagttttaaccctgtctgttcttcttactgaacagGAAATTCCAGATAACGAGTTTGAGAAGCGCATCAGGCCAGAGGTTATACCAGCCAGTGAGATAGGAGTGACTTTTGATGACATTGGAGCCCTGGCTGACA
| ||| | |||| | | | | | | | |||||| || ||| | || ||| | || | | || | | || ||| | | | || ||||| ||||||||||||| || ||||||||||| |||||||| | |||||| | || || || ||| ||||| ||| | | ||
---------------------------------acacttcatatctaaaggtgtagaaacacccctttgaattttg--cttactatcacttttttcctatt-ctgtaaatttta---tgtcaaac--atttgcactttc-----agGAAGTTCCTCTTGATAATGAGTTTGAGAAGCAAATAAGGCCAGAGGTAATACCAGCAAATGAGATTGATGTCACATTCTCTGATATTGGTGCCTTAGATG---
upper sequence: LOC_Os05g50750.3 (Oryza sativa), 3'ss of exon 10
lower sequence: AT4G28000.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaagtttagtattcagtatttcagttccttgtgccctttgttctacgaattcatagcttgctaccaagactgtaaagctactatttgttctttgtgaccattgcaaagtctaaagttttaaccctgtctgttcttcttactgaacagGAAATTCCAGATAACGAGTTTGAGAAGCGCATCAGGCCAGAGGTTATACCAGCCAGTGAGATAGGAGTGACTTTTGATGACATTGGAGCCCTGGCTGACA
|| | || || || | | ||| | | ||| |||| | | || ||| | | | | || | | ||| ||| ||||| || || ||||||||||| || ||||||||||| ||||| | |||||| || |||||||||| ||| || || | |||| ||
-----------------------------------------------------gtacatgtaaactaatacatatgattcagcattgataccttgatgtgtttgcctgaac-ataggtttgattttccttatcctgtcaatgtagGAGGTGGCTCCTGATAATGAATTCGAGAAGCGCATAAGACCAGAGGTTATCCCAGCAAATGAGATTGGTGTGACTTTTGCTGATATAGGTTCACTGGATG---
upper sequence: LOC_Os05g50750.3 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv16s0050g01830.t01 (Vitis vinifera), 3'ss of exon 10
gtaagtttagtattcagtatttcagttccttgtgccctttgttctacgaattcatagcttgctaccaagactgtaaagctactatttgttctttgtgaccattgcaaagtctaaagttttaaccctgtctgttcttcttactgaacagGAAATTCCAGATAACGAGTTTGAGAAGCGCATCAGGCCAGAGGTTATACCAGCCAGTGAGATAGGAGTGACTTTTGATGACATTGGAGCCCTGGCTGACA
| | || | || ||| | | || ||||| ||| || | | | ||| ||||| |||| | ||| | || || | || || ||||||| ||| || |||||||||||||| ||||| | | ||||||||||| | ||||| |||||||| ||| ||| ||
-----------------------------aaggaggttcccttgcatttgttttcccctttttgttgaag--aaaattttactaagaaaattttccgatattcccttactct-----tttaat------tgtt-tcgctac--agTTGGTTCCACCTTACAATGAATTTGAGAGGCGTATAAGGCCAGAGGTTATCCCAGCAAATCAGATAGGAGTGGCATTTGAGGACATTGGTGCCTTGGATG---
upper sequence: LOC_Os05g50750.3 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv02s0025g00650.t01 (Vitis vinifera), 3'ss of exon 11
gtaagtttagtattcagtatttcagttccttgtgccctttgttctacgaattcatagcttgctaccaagactgtaaagctactatttgttctttgtgaccattgcaaagtctaaagttttaaccctgtctgttcttcttactgaacagGAAATTCCA---GATAACGAGTTTGAGAAGCGCATCAGGCCAGAGGTTATACCAGCCAGTGAGATAGGAGTGACTTTTGATGACATTGGAGCCCTGGCTGACA
|||||| |||| | | | |||| | ||||| | || | | || ||| | || || || | ||| | | || | |||||||| |||| || || || ||||||||||||||||| |||||||| || ||||| |||||||| || ||||| |||| ||| ||||| ||| ||| ||
-------------------------------------tttgttt----aatttacaaaaaat-----aatctgtttcaatcgcatttgattttcttaccttttttgtagttttaacgttgaaag--gcctgctatattttcctaacagGAAGTTCCTCCTGACAATGAATTTGAGAAGCGCATCAGACCAGAGGTCATCCCAGCTAGTGAGATTGGTGTGACATTTGCTGATATTGGTGCCATGGATG---
upper sequence: LOC_Os05g50750.3 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv16s0050g01850.t01 (Vitis vinifera), 3'ss of exon 12
gtaagtttagtattcagtatttcagttccttgtgccctttgttctacgaattcatagcttgctaccaagactgtaaagctactatttgttctttgtgaccattgcaaagtctaaagttttaaccctgtctgttcttcttactgaacagGAAATTCCA---GATAACGAGTTTGAGAAGCGCATCAGGCCAGAGGTTATACCAGCCAGTGAGATAGGAGTGACTTTTGATGACATTGGAGCCCTGGCTGACA
| || ||| | || | || | | || | || | | | | | || ||||| | || ||| || | |||| |||| || |||||| ||||| || || || ||||||||||| || |||||||||||||| ||||| | ||||||||||||||| |||||||| || || || || ||
------------------------gatcacaatgctgat--ttttgtaaaagaaaattttattgggaaaattttccatcattcccttactcttt-taactgttg---------aactgttaat------tgtttccctc------cagGAAGTTCCACCTGACAATGAATTTGAGAAGCGTATAAGGCCAGAGGTTATCCCAGCGAATGAGATAGGAGTGACATTTGATGATATCGGTGCTTTGAGTG--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgaccattgcaaagtctaaagttttaaccctgtctgttcttcttactgaacagGAAATTCCAGATAACGAGTTTGAGAAGCGCATCAGGCCAGAGGTTATACCAGCCAGTGAGATAGGAGTGACTTTTGATGACATTGGAGCCCTGGCTGACA
ttcttac putative branch site (score: 2)
ccctgtctgttcttct CT-rich tract
taaagttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttagtattcagtatttcagttccttgtgccctttgttctacgaattcatagcttgctaccaagactgtaaagctactatttgttctttgtgaccattgcaaagtctaaagttttaaccctgtctgttcttcttactgaacagGAAATTCCAGATAACGAGTTTGAGAAGCGCATCAGGCCAGAGGTTATACCAGCCAGTGAGATAGGAGTGACTTTTGATGACATTGGAGCCCTGGCTGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG