Sequence
atgc intronic sequence ATGC exonic sequenceAGGCCTCTGACATGGTTCTTGCTGATGACAATTTTAGTACCATTGTTGCGGCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAGgttagtgatctcagagcctgtttttgttgttgttctcactttttgcttcaacacttgcttttgtcacttctattttggcagaaacaaacagactaatgct...
Basic information
species | Oryza sativa |
transcript | LOC_Os05g02940.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g02940.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G056014_T01 (Zea mays), 5'ss of exon 6
AGGCCTCTGACATGGTTCTTGCTGATGACAATTTTAGTACCATTGTTGCGGCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAGgttagtgatctcagagcctgtttttgttgttgttctcactttttgcttcaacacttgcttttg--tcacttctattttggcagaaacaaacagactaatgct---------------
|||| ||||||||||| | ||||| ||||||||||| ||||| ||| | ||||| ||||||||||| || || ||||||||||||||||||||||| |||| ||| | |||| || ||| || |||||| |||||| | | || | | ||||| | |||| || ||| || | | |
AGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACCATAGTTTCTGCAGTCGGTGAAGGAAGATCGATCTACAACAACATGAAAGCTTTCATAAGgtctgtg----ctgagcttgctttgattattgttcacactttgtagt---actcgtacttttcgcccccttcccttgtgggcattcttgacgtccctgtcttcctcggctgccgcag
upper sequence: LOC_Os05g02940.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT1G07670.1 (Arabidopsis thaliana), 5'ss of exon 7
AGGCCTCTGACATGGTTCTTGCTGATGACAATTTTAGTACCATTGTTGCGGCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAGgttagtgatctcagagcctgtttttgttgttgttctcactttttgcttcaacacttgcttttgtcacttctat-tttggcagaaacaaacagactaatgct
|||| |||||| |||| | || ||||| ||||| || ||||||||||| || ||||||||||| ||||| || || ||||||||||| || |||||||||| ||| ||| | | | | | | ||| | | |||| | | | | ||| ||| | || | | || | |
AGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGGCCTTCATCAGgtgagtcttcttatgttacatatgtatgcctcttcctatgggtggcttgagt-tatacatacaaaccttatatatctgactatgatgaataaaag------
upper sequence: LOC_Os05g02940.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT1G07810.1 (Arabidopsis thaliana), 5'ss of exon 7
AGGCCTCTGACATGGTTCTTGCTGATGACAATTTTAGTACCATTGTTGCGGCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAGgttagtgatctcagagcctgtttttgttgttgttctcactttttgcttcaacacttgcttttgtcacttctattttggcagaaacaaaca-gactaatgct--
|||| |||||||||||| | || ||||| ||||| || ||||||||||| || || |||||||| ||||| || || ||||||||||| || |||||||||| ||| ||| | | | | | | | | | | || | | | | || | | ||| | | | | | || |||
AGGCATCTGACATGGTTTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTAGGTGAAGGCAGGTCCATCTATAACAACATGAAGGCCTTCATCAGgtgagtcttctactatcacatatatatatatatgccta---ttcgtattgatggcttgagttatacatactaagcctatatatatgactatgatgaataaaag
upper sequence: LOC_Os05g02940.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv06s0004g03900.t01 (Vitis vinifera), 5'ss of exon 6
AGGCCTCTGACATGGTTCTTGCTGATGACAATTTTAGTACCATTGTTGCGGCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAGgttagtgatctcagagcctgt-----ttttgttgttgttctcactttttgcttcaacacttgcttttgtcacttctattttggcagaaacaaacagactaatgct
| |||||||||||||| | || ||||| ||||||| || || ||||| || ||||||||||| || || ||||||||||| ||||| ||||| |||||||| | | | || | || | | ||| | ||| | | | || | | | || || || |
AAGCCTCTGACATGGTCTTGGCAGATGATAATTTTAACACAATAGTTGCTGCTGTTGGTGAAGGCAGATCCATTTACAACAATATGAAGGCTTTTATCAGgtttgattcttttgtgcataagaaaattcagctacctggtaggcttacaaaattgacatataatacaattacctagaatgtgaagagtgttcactgagaa-----
upper sequence: LOC_Os05g02940.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv08s0040g02830.t01 (Vitis vinifera), 5'ss of exon 6
AGGCCTCTGACATGGTTCTTGCTGATGACAATTTTAGTACCATTGTTGCGGCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAGgttagtgatctcagagcct--gtttttgttgttgttctcactttttgcttcaacacttgcttttgtcacttctattttggcagaaacaaacagactaat-gct-
| |||||||| ||||| | || || || ||||||||||| || ||||| || ||||| ||||| | ||||| |||||||| ||||| ||||| |||||||| | | | | || | ||| || | || | | | | | | || | | | || || ||| | || | ||
AAGCCTCTGATATGGTGTTGGCAGACGATAATTTTAGTACAATAGTTGCTGCTGTTGGGGAAGGGCGATCTATCTACAACAATATGAAGGCTTTTATCAGgtttatttctttgcattcctggtctctgtggtctgtgacagatgcagatctgagataagattat----ttgtttttgtgacagtggtggagttcttagtcacta
upper sequence: LOC_Os05g02940.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S80_36V6.1 (Physcomitrella patens), 5'ss of exon 6
AGGCCTCTGACATGGTTCTTGCTGATGACAATTTTAGTACCATTGTTGCGGCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAGgttagtgatctcagagcctgtttttgttgttgttctcactttttgcttcaacacttgcttttgtcacttctattttggcagaaac-aaacagactaatgct----------
| || |||||||||| || || || |||||||| || || || || || || ||||| || || | | |||||||||||||||||||| ||||||||||| ||| | | | || | || | ||| | | | | | | ||| | | | ||||| ||| | | |||
AAGCTGCTGACATGGTGCTGGCAGACGACAATTTCAGCACAATCGTGGCAGCTGTTGGAGAGGGTCGTGCAATTTACAACAACATGAAAGCCTTCATCAGgtt-------tcatattgttccactcccgtcaactttacgtaatgcatgagtccctattctcgtc-ttcaagctattccagaacttgaactgcatcatgtggattctacag
upper sequence: LOC_Os05g02940.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S248_28V6.1 (Physcomitrella patens), 5'ss of exon 6
AGGCCTCTGACATGGTTCTTGCTGATGACAATTTTAGTACCATTGTTGCGGCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAGgttagtgatctcagagcctgtttttgttgttgttctcactttttgcttcaacacttgcttttgtcacttctattttggcag-aaacaaacagactaatgct
|||| | |||||||| ||||| |||||||||||||| || ||||| || || ||||| ||||| | ||||| |||||||||||||| || ||||| |||| ||||| | | | | | || ||| | | || || | | | | | || | | | | | ||||
AGGCAGCCGACATGGTGCTTGCAGATGACAATTTTAGCACTATTGTGGCAGCCGTTGGAGAAGGTCGTTCTATATACAACAACATGAAGGCCTTCATTAGgtgcgtgattttatactaaggatgattttttgagtggagtatt---ttggaaattgagtaccagaagtttgactgaagttgtggatctacag---------
upper sequence: LOC_Os05g02940.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ29960 (Selaginella moellendorffii), 5'ss of exon 6
AGGCCTCTGACATGGTTCTTGCTGATGACAATTTTAGTACCATTGTTGCGGCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAGgttagtgatctcagagcctgtttttgttgtt-gttctca-ctttttgcttcaacacttgcttttgtcacttctattttggcagaaacaaacagactaatgct
||||| | ||||||||||| ||||| || || || || || ||||| || |||| |||||||| || ||||||| |||||||||||| |||||||||| | | | | | || |||| | || | | || |||| | ||| | | |
AGGCCGCAGACATGGTTCTCGCTGACGATAACTTCAGCACGATTGTGAGTGCCGTTGCCGAAGGAAGATCGATTTACAGCAACATGAAAGCATTCATCAGgt--gcgcttagtgtgtctcgatttgatatttgctgacaactttctttttcgtcgttag-------------------------------------------
upper sequence: LOC_Os05g02940.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ25083 (Selaginella moellendorffii), 5'ss of exon 6
AGGCCTCTGACATGGTTCTTGCTGATGACAATTTTAGTACCATTGTTGCGGCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAGgttagtgatctcagagcctgtttttgttgttgttctc-actttttgcttcaacacttgcttttgtcacttctattttggcagaaacaaacagactaatgct
||||| | ||||||||||| ||||| || || || || || ||||| || |||| |||||||| || ||||||| |||||||||||| |||||||||| | | | | | || |||| ||| | | ||||| | ||| | | |
AGGCCGCAGACATGGTTCTCGCTGACGATAACTTCAGCACGATTGTGAGTGCCGTTGCCGAAGGAAGATCGATTTACAGCAACATGAAAGCATTCATCAGgt--gcgcttagcgtgtctcgatttgaatttgctgacgactttctttttcgtcgttag-------------------------------------------Mapped 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|29685095|gb|CB681370.1|CB681370EST: GAAGGAAGGTCTATTCACAACAACATGAAAGCTTTCATCAG ATACATGATTTCCTCAAACATTGGTGAAGTTGCGTCAATTTTCCTAACTTC
genomic: GAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAGgttagtgatc ... actgctgcagATACATGATTTCCTCAAACATTGGTGAAGTTGCGTCAATTTTCCTAACTTC
EST:
gi|12622875|gb|AU173088.1|AU173088EST: GCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAG ATACATGATTTCCTCAAACATTGGTGAAGTTGCGTCAATTTTCCTAACTTC
genomic: GCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAGgttagtgatc ... actgctgcagATACATGATTTCCTCAAACATTGGTGAAGTTGCGTCAATTTTCCTAACTTC
EST:
gi|87016976|gb|CI286112.1|CI286112EST: GCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAG ATACATGATTTCC
genomic: GCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAGgttagtgatc ... actgctgcagATACATGATTTCC
EST:
gi|8857836|gb|AU095154.1|AU095154EST: GCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAG ATACATGATTTCCTCAAACATTGGTGAAGTTGCGTCAATTTTCCTAACTTC
genomic: GCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAGgttagtgatc ... actgctgcagATACATGATTTCCTCAAACATTGGTGAAGTTGCGTCAATTTTCCTAACTTC
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),
71 (downstream exon)
Score:
16AGGCCTCTGACATGGTTCTTGCTGATGACAATTTTAGTACCATTGTTGCGGCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAGgttagtgatc ... actgctgcagATACATGATTTCCTCAAACATTGGTGAAGTTGCGTCAATTTTCCTAACTTCTGCTCTGGGTATTCCTGAGGGGTTGATACCGGTTCAACTTCTATGGGTA
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGGCCTCTGACATGGTTCTTGCTGATGACAATTTTAGTACCATTGTTGCGGCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAGgttagtgatctcagagcctgtttttgttgttgttctcactttttgcttcaacacttgcttttgtcacttctattttggcagaaacaaacagactaatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa