Sequence
atgc intronic sequence ATGC exonic sequencegtaaccttctcgctcgcttctcctctcctccattcccgtctccgattcgccttctcgtgacgcctcctctgactgactctcgttggcgcttctgtccccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g58050.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G130544_T02 (Zea mays), 3'ss of exon 1
gtaaccttctc-gctcgcttctcctctcctccattcccgtctccgattcgccttctcgtgacgcctcctctgactgactctcgttggcgcttctgtccccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG
||||||||||| ||| ||||||| | | | | || | | | || | || | ||||||| || || ||||| ||||||||||||||||||||||||||||||||||| ||||||||| |||||||||||||||| |||||||||||||||||||||||||| | ||||| |||||||
gtaaccttctccactcacttctccccattgct-tctcggtgtgcagatatttttatagtttc-----------ctgactccg--tgacg--tctgtggccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCATATCCTGCGTTTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCAATCAAGG
upper sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 1
gtaaccttct-cgctcgcttctcctctcctccattcccgtctccgattcgccttctcgtgacgcctcctctgactgactctcgttggcgcttctgtccccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG
||||||| || | || | |||| | || | || ||| | | || | || || | || || || || || |||| |||||||||||||||||||| ||||||||||| || || ||||||||||||||||||||||| |||||||||||||||||||||||||| | |||||||| ||||
gtaacctcctacacttattcctccccgcc--gactctcgttgtgcagatg--tttttgtatcgtgttct------gattcc--gtgacga--ctgttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG
upper sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA20G30730.1 (Glycine max), 3'ss of exon 1
gtaaccttctcgctcgcttctcctctcctccattcccgtctccgattcgccttctcgtgacgcctcctctgactgactctcgttggcgcttctgtc--cccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG
| || | | | || | | | | | | | || | | | ||| || ||| ||| | | |||||||| | || ||||| ||||||||||| || ||| | ||||||| ||||| ||||||||||||||||| |||||||| || ||||| ||||| |
gaaatcaagatttttgaaactgactcttgttttggatatgtaaaaattgtgcatttgtaat-----tttggtttgaaactgattgatccttgtcttgttttatagTCGCTGGTGGCAAACGAGGATTTCCAGCACATACTTCGTGTTTTGAACACGAACGTAGATGGGAAGCAGAAGATAATGTTCGCTCTTACCTCAATCAAAG
upper sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G36880.3 (Glycine max), 3'ss of exon 1
----------gtaaccttctcgctcgcttctcctctcctccattcccgtctcc------gattcgccttctcgtgacgcctcctc--tgactgactctcgttggcgcttctgtccccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG
| | || | || | || | || | | | | ||||| || | || | | || | ||||| | || | | ||| |||||| ||| | || ||||| ||||||||||| |||||| |||||||||||||||| ||||||||||||||||| |||||||| | |||||||||||||
gtgcgctcccattattttattgcacctctcccttcacaacgttgattgaacaataaaaggattctattttgaggaacccttaatcgataactgatttctttttttgtgtgtgtt---gcagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTGGATGGGAAGCAGAAGATAATGTTCGCAATGACCTCCATCAAGG
upper sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G36610.3 (Glycine max), 3'ss of exon 1
--------gtaaccttctcgctcgcttctcctctcctccattcccgtctcc------gattcgccttctcgtgacgcctcctc--tgactgactctcgttggcgcttctgtcc-ccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG
| | | |||| | || | || | | | | ||||| || | || | | || | |||| | | || || ||| |||||| ||| | || ||||| ||||||||||| |||||| |||||||||||||||| ||||||||||||||||| |||||||| | |||||||||||||
gcgctctcattatttcatcgcacctctcccttcacaacgttgattgaaaagaaaaaagattcaattttgaggaacccttaatcgatatctgattttttttt---tttgtgtgtgttgcagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTGGATGGGAAGCAGAAGATAATGTTCGCAATGACCTCCATCAAGG
upper sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G08690.1 (Glycine max), 3'ss of exon 1
-----------------------------------gtaaccttctcgctcgcttctcctctcctccattcccgtctccgattcgcc-ttctcgtgacgcctcctctgactgactctcgtt---ggcgcttctgtccccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG
|| | | || | | || || | | | | || || | || | | | || || || | || | || || | ||||| ||| | || ||||| ||||||||||| |||||| |||||||||||||||| ||||||||||||||||| |||||||| |||||||| ||||| |
gtacgatttcagcgtttccgaattgattttgataaacaaagattcttcaaaagattcgttttatcttttggcaatttcaaaaggcgatttttttggctctgtttttggaggagtcacattttaaatggttttg--cttacagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTAGATGGGAAGCAGAAGATAATGTTCGCTCTCACCTCTATCAAAG
upper sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G36610.2 (Glycine max), 3'ss of exon 1
----------gtaaccttctcgctcgcttctcctctcctccattcccgtctcc------gattcgccttctcgtgacgcctcctc--tgactgactctcgttggcgcttctgtcc-ccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG
| | | |||| | || | || | | | | ||||| || | || | | || | |||| | | || || ||| |||||| ||| | || ||||| ||||||||||| |||||| |||||||||||||||| ||||||||||||||||| |||||||| | |||||||||||||
gtgcgctctcattatttcatcgcacctctcccttcacaacgttgattgaaaagaaaaaagattcaattttgaggaacccttaatcgatatctgattttttttt---tttgtgtgtgttgcagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTGGATGGGAAGCAGAAGATAATGTTCGCAATGACCTCCATCAAGG
upper sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA20G30970.1 (Glycine max), 3'ss of exon 1
-----------------gtaaccttctcgctcgcttctcctctcctccattcccgt---ctccgattcgccttctcgtgacgcctcc-tctgactgactctcgt-tggcgct-tctgtccccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG
||||| || ||| | | | | || || || | | || | || | | || | | ||| | | |||||| ||| | || ||||| ||||||||||| |||||| |||||||||||||||| ||||||||||||||||| |||||||| | |||||||||||||
gtacgttcccatttcatcgaacctctccgagcgcgacgttaattgaaaaaaaaggattactttgaggaacccttaatcggtaactgaatttgttttttttgtgtgttgtgctgtgttgtgttgcagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTGGATGGGAAGCAGAAGATAATGTTCGCTATGACCTCCATCAAGG
upper sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv18s0072g00060.t01 (Vitis vinifera), 3'ss of exon 2
gtaaccttctcgctcgcttctcctctcctccattcccgtctccgattcgccttctcgtgacgcctcctctgactgactctcgttggcgcttctgtcc--ccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG-------------------
| | | || || | |||| | | |||| | | | | | || | ||| ||| || |||||||| | || || || ||||||||||| ||||| | |||||||| ||||| |||||||| |||||||| ||||| || ||||| || |||||||
-----------------gtaatcagggtttcaatctcttctc-gttcttcctttagaatgcctataatttaatgtacgtttgttcaatctttcgttgggttacagtcgctagtggcgaacgaagAATTCCAGCACATATTGCGTGTCCTGAACACGAACGTGGATGGGAAACAGAAGATAATGTTTGCCCTCACGTCAATCAAGGGTATTGGGAGGCGATTCGC
upper sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv05s0020g03450.t01 (Vitis vinifera), 3'ss of exon 1
gtaaccttctcgctcgcttctcctctcctccattcccgtctccgattcgccttctcgtgacgcctcctctgactgactctc--gttggcgcttctgtccccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG
| | || | |||| | || | || |||| ||| || | | | | | ||| | | | |||||| || | || ||||| || |||||||| || ||| |||| ||||||||||||||||||||||||||||||||||| || ||||| ||||||||||
-------------gtgagtgggcttgttttcatttctgtt---aaatcaa-ttcttgtgtcgaatatggttgtttgttgttatgttaatgaattggattttgcagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG
upper sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S242_94V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------gtaaccttctcgctcgcttctcctctcctccattccc-gtctccgattcgccttctcgtgacgcctcctctgactg----actctc-----gttggcgcttctgtccccg---------------cagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG
| ||| | | | | || || ||| ||| | | |||| | | | | || || | || || || ||| | || ||||| | | |||||||| || || || ||||| || |||||||| || ||| |||||||||| ||||||||||| |||||||||||||| || || || || || ||||
gtgcgtgttcatcgcttcctccccatgcagctttcgtcgactcgtttctttgcgtacgatgagattgttatttttttttcttccaaatgttgtacacttctagggttcgtgcatctgtgactgaaagctggttgtgaacagTCGCTCATTGCGGGCGAGGAATTTCAGCACATTCTTCGTGTGCTGAACACTAACGTCGATGGACGTCAGAAGATCATGTTTGCCCTGACTTCGATTAAGG
upper sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S14_433V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------------------------------gtaaccttctcgctcgcttctcctctcctccattcccgtctc-cgattcgccttctcgtga-cgcctcctctgactga-----ctctcgttggcgcttctgtccccg-----cagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG
|| || | | || | | | | || || | | ||| | ||| || | || | | | || | || | | || | |||||||||||||| || ||||| || |||||||| || ||| || ||||||| ||||||||||| || ||||| ||||| || | |||||||| ||||
gtttgtgctcctctgctgttgcgtatatctgtggtgtcgttttttgtttggtactgagttctgggtgtgtttttttttttttttttttttttttttttttttggtttttcaatttttaggttaatgatcgtttgctagggttaattgggctgtgactgaggttggtggcggttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACTAACGTCGATGGACGTCAAAAGATTATGTTTGCCTTGACCTCCATTAAGG
upper sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S215_71V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------gtaaccttctcgctcgcttctcctctcctccattcccgtctccg----attcgccttctcgtg---acgcctcctctgactgactctcgttggcgcttctgtcc-----ccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG
|| ||| | ||| | || | || ||| | || ||| | | | | ||| || | ||||||| | | | | | | | ||| ||||||||| || || || ||||| ||||||||||| || ||| | ||||| ||||||||||||||| |||||||| ||||| || || |||||||||||||
gtgtgtctgatctgcctcgtccttgtcattgtgctgctcttcttggctcttattcagtgctatcttcgtgttcgtgaaattttatgtttagggtttacgtctt-tgtgactgaaagttggttgtgtgtgtttccgatgttggcagTCGCTCATTGCGGGCGAGGAGTTCCAGCACATTCTTCGTGTTCTGAATACCAACGTCGATGGGCGTCAGAAGATTATGTTTGCCCTAACCTCCATCAAGG
upper sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S14_438V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------gtaaccttctcgctcgcttctcctctcctccattcc---cgtctccgattcgccttctcgtgacgcctcctc-tgactgactctcgttggcgcttctgtccccg--cagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG
|||| | || | ||| || || || || | ||| ||| | || || ||| | | ||| | || | ||||||| ||||| || || || || || || || || ||| ||||||| || ||||||||||| |||||||||||||||||| || |||||||| || |
gtgggtagtttctcccacctgtgctacacgtaaaaatttcagtt-tttcggttccgttctgtttggagtgttttttgctcgactttagggtgtgcaggttcatgatctaaattggttcagaatggtgggtgtgactagTCGCTCATCGCGGGTGAAGAGTTTCAACATATTCTTCGTGTGCTGAATACAAACGTCGATGGACGGCAGAAGATCATGTTCGCCCTGACCTCCATTAAAG
upper sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 1
gtaaccttctcgctcgcttctcctctcctccattcccgtctccgattcgccttctcgtgacgcctcctctgactgactctcgttggcgcttctgtccccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG
| | |||| ||| | | | | | | ||| ||||| ||||| |||||| ||| | | ||||| ||||||||||| || ||| |||| ||||| || || || ||| ||||||||| ||||||||||| || ||||||||||
--------------------------------------------gtatga-ttcttgtgttgggtgttg-aaataatcctc--cggcgcctctgttttggcagTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|87038489|gb|CI193111.1|CI193111EST: CGCCGCCGCCGCCATG TCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACC
genomic: CGCCGCCGCCGCCATGgtaaccttct ... gtccccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACC
EST:
gi|3763273|gb|AU030025.1|AU030025EST: CCGCCGCCGNCCAATG TCGCTNATCNCCGGGGAGGACTTCCACCACATCCTGCGTCTGCTGAACAC
genomic: CCGCCGCCG-CC-ATGgtaaccttct ... gtccccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACAC
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
75 (upstream exon),
75 (downstream exon)
Score:
208GCCTCCGAAGCCCTAGCTCCTCCCGCCGCCGCCGCCGCCGCCGCCGCCGCCTCTCCACTCGAGAGACCCAGCCGCCGCCGCCGCCGCCGCCGCCATGgtaaccttct ... gtccccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccttctcgtgacgcctcctctgactgactctcgttggcgcttctgtccccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG
gactgac putative branch site (score: 208)
cttctgtcccc putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaccttctcgctcgcttctcctctcctccattcccgtctccgattcgccttctcgtgacgcctcctctgactgactctcgttggcgcttctgtccccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA