Sequence
atgc intronic sequence ATGC exonic sequencegtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
Basic information
species | Oryza sativa |
transcript | LOC_Os05g12150.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G143747_T01 (Zea mays), 3'ss of exon 1
gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
|||||||| | | | || | || || | | || | || || | || || | | | | | | || ||| | || | | | | | ||| |||||| | | | ||||| || || || ||||| || || || ||||| ||||| || ||||| || |||| |||||||||||||||||||||||||||||| |||| | ||||
gtatgcacaacgcgtctctcgttgcattaattagcaa------gcaagcattgtgaccatgg-cagctgggttcgtcgctgtgctgaacacgatttttgt----tttggttc----ttttatgttttgtctcgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGGTGACCATGATGTCGTGGGGCATCCTGGAGT
upper sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA05G36930.1 (Glycine max), 3'ss of exon 1
gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
| | |||| | | | || | ||| | | | | | | ||| || | ||||| ||| | || || | ||||| ||||| |||||||| || |||||||||||||||||||| ||||| ||||| || |||||||| || || || ||||||||||||||||| | || |
--------------------------------------gtaagcttttcaa---ctctttttttagtttagtttagtt-tctcactttcctcacccaaattcag---gttacaaattattg-atgttaaattata---cagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGGTTACCCATGGCGTTTACCGTTACGATGATGTCGTGGAGCATCATTGAAT
upper sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G02610.1 (Glycine max), 3'ss of exon 1
gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtcttt-cagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
| ||| || | | | | | | | | ||| | | | | | | || |||| |||| | | ||||| ||||| |||||||| || |||||||||||||||||||| ||||| ||||| || |||||||| || || || ||||||||||||||||| | || |
--------------------------------------------------------gtaagtttaagaactcttttactttagtttactca--cccaaattctttctagtcctagttttcatgttgatgttaaattatgcagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGGTTACCCATGGCGTTTACCGTTACGATGATGTCGTGGAGCATCATTGAAT
upper sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G64390.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------------------------gtatgcaccattctaccttcaaatct---ttgatcaaaaccatgatgccatcaat-ggcattgtgttcaattt--gttcaggagatatgatgagttgggttctaatggagtgcaatgca--aatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
|| ||| | || | | | | | | || || | || | | | | ||| || | | ||| |||||| | | | | || | | | || || || | | | | || | ||| |||||| |||| || |||||||| || || || || |||||||| || ||||| || || ||||| ||||||||||| |||||| ||||||| | | ||||
gtatgtctctccctctctgtctctctctttctagattttgtttccgacattgt-tgctctgttttccacttgattttgagtttattcagacaacatttcagtaaattagctatagatctgttttccgttcagacaacgtcgtcaccaacattgt--tcgtgtttcatacagtactaactagaatcttttgtgttgatcagGTGAATCTGGTCGGAGGTTACTACGACGCCGGAGACAATGTGAAATTTGGATTACCGATGGCTTTCACGGTGACGATGATGGCGTGGAGTGTGATTGAGT
upper sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0025g01380.t01 (Vitis vinifera), 3'ss of exon 3
------gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
|| ||| || | || |||| | ||| || |||| || | ||| ||| | | | || ||| ||| | | || ||| | | ||| || ||| |||| ||| | |||| ||||| || ||||| |||||||||||||| |||||||| |||||||| | || ||||| ||||| || || |||||||| ||||||||| | ||||
gtaagttcattttccactccaactcaaaatttctgaa-aagcccattgtgg-aacaagacaattataattgaattattcc----atacaaccaaatgtgttgaagttttttgctat---aatctttgagtt----------atgtagGTGGATCTGGTGGGAGGATATTATGATGCAGGTGACAATGTGAAGTTTGGCCTACCCATGGCATTCACCGTTACAATGATGTCATGGAGCATAGTGGAGT
upper sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S176_127V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagt-tgggttctaatgg--agtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
||| | | | || | | ||| ||| | | ||| | | | || | | ||||||| | | || | || | || || | | | ||| | |||| | |||| ||||| ||||| |||||||| ||||| || ||||||||||||||||| ||||| |||| ||||| || |||||| |||||||||| | | ||||
gtaagaccttcgtttcgcgttctagatgggtgactgttttatcttaagcatagaaaaagttgtgaagaggatgtagacat-gctcgccagctgacaattaaatatgatatatgtaggatatagtcattggttcatttgctttacgattatttgtacttgtaatgtagGTGGATCTGGTTGGTGGTTATTACGATGCTGGTGACAATGTCAAGTTTGGCTTGCCTCTGGCATTCACTGTTACCATGCTGTCGTGGAGTGTTCTTGAGT
upper sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S37_355V6.1 (Physcomitrella patens), 3'ss of exon 1
gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgtt-caatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
| || | || || | || | | ||| ||| || | | | | || | || || | || | || || || | |||| ||||| | | ||||||| ||| |||||||| || |||||||| ||||||||||||| ||| |||| |||||||| || | || ||| | || ||||| || | || |
--------------gtaagtggcacattccttgaactcacaacagtttc--tcgtgttgcgttgcagtaccgcaatgtcgcagaataa--tgtgtcgtgatagctcacactgt--atctgtgtggcgttgtt--ccgtgtagGTTGACCTTTCGGGAGGTTACTACGATGCAGGAGACAATGTCAAGTATGGTCTGCCGATGGCGTTTACCATTACTATGCTCTCTTGGAGTGTAATTGAAT
upper sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ12750 (Selaginella moellendorffii), 3'ss of exon 1
gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
| | | | ||| || | | || | | || | | | | || ||| || || || || || | || | ||| || || ||||| ||| | |||||||| ||||| || || || ||||||||||||||||| |||| ||||| ||||| | |||||||||||||||||| | ||||
--------------------------------atagata-gctgcattcgaggatatctttccc---tttcggatgtgcctttgcgaattgagtactt-tgcgttgtggtg--attgatggtggcgctg--gaactaccagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGCCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGT
upper sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ13916 (Selaginella moellendorffii), 3'ss of exon 1
gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
| | | ||| || | | || | | || | | | | || ||| || || || || || | || | ||| || || ||||| ||| | |||||||| ||||| || || || ||||||||||||||||| |||| ||||| ||||| | |||||||||||||||||| | ||||
--------------------------------gtagata-gctgcattctaggatatctttccc---tttcggatgtgcctttgcgaattgagtactt-tgcgttgtggtg--attgatggtggcgctg--gaactaccagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGTCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGTMapped 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|86900869|gb|CI304074.1|CI304074EST: GGGTCTCCTGGAGAGCCAGCTCTGGCCTCTTTGATGGAAAGGCCAATGGA GTTGATCTTGTTGGAGGTTATTATGATGC
genomic: GGGTCTCCTGGAGAGCCAGCTCTGGCCTCTTTGATGGAAAGGCCAATGGAgtatgcacca ... tgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGC
EST:
gi|88364046|gb|CI610390.1|CI610390EST: GGGTCTCCTGGAGAGCCAGCTCTGGCCTCTTTGATGGAAAGGCCAATGGA GTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGG
genomic: GGGTCTCCTGGAGAGCCAGCTCTGGCCTCTTTGATGGAAAGGCCAATGGAgtatgcacca ... tgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
ttctaat putative branch site (score: 2)
tttttgtttgtctttc putative PPT
tttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA