Sequence
atgc intronic sequence ATGC exonic sequencegtatgcttgattgacttgttaacaccttagaacttttaggattgatttcatagctttttttttccttgttaaagatttctgttaaaaccctctggatagtgattttcttgcttttgtgtattctatggagaagatctctagttcagatatatatgtggttttgcagATTGCTGATTTCTGGAAAGAAGCTCAGATTCTAAGTTCACTTCATCATCCAAATGTGGTTTCATTTTATGGTGTAGTTCGTGACGGTCCTGATGGAAGCT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g54510.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g54510.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G052658_T01 (Zea mays), 3'ss of exon 3
gtatgcttgattgacttgttaacaccttagaacttttaggattgatttcatagctttttttttccttgttaaagatttctgttaaaaccctctggatagtgattttcttgcttttgtgtattctatggagaagatctctagttcagatatatatgtggttttgcagATTGCTGATTTCTGGAAAGAAGCTCAGATTCTAAGTTCACTTCATCATCCAAATGTGGTTTCATTTTATGGTGTAGTTCGTGACGGTCCTGATGGAAGCT
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------------------------------------------------------------aatgatattttgagctatccagctgggctgaggagaaagtaaat---ttgaacatat-ttttctgttcaaaatgattctagttcagatttatcta--attttgcagATTGCGGATTTCTGGAAAGAAGCTCTGATCCTAAGCTCACTCCATCATCCAAATGTGGTTTCATTTTATGGTGTAGTTCGTGATGGTCCAGATGGAAGCT
upper sequence: LOC_Os02g54510.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G039106_T02 (Zea mays), 3'ss of exon 2
gtatgcttgattgacttgttaacaccttagaacttttaggattgatttcatagctttttttttccttgttaaagatttctgttaaaaccctctggatagtgattttcttgcttttgtgtattctatggagaagatctctagttcagatatatatgtggttttgcagATTGCTGATTTCTGGAAAGAAGCTCAGATTCTAAGTTCACTTCATCATCCAAATGTGGTTTCATTTTATGGTGTAGTTCGTGACGGTCCTGATGGAAGCT
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-----------------------------------------------------------tgaaaatatttggaggt----attaaaatgggctgaggagag-taaatttgaacttatgc-ttcagtgcaaaatgattctagttcagctttatcta-aattttgcagATCACGGATTTCTGGAAAGAAGCTCTGATCCTAAGCTCACTTCATCATCCAAATGTGGTTGCATTTTATGGTGTAGTTCGTGATGGTCCAGATGGAAGCT
upper sequence: LOC_Os02g54510.3 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgcttgattgacttgttaacaccttagaacttttaggattgatttcatagctttttttttccttgttaaagatttctgttaaaaccctctggatagtgattttcttgcttttgtgtattctatggagaagatctctagttcagatatatatgtggttttgcagATTGCTGATTTCTGGAAAGAAGCTCAGATTCTAAGTTCACTTCATCATCCAAATGTGGTTTCATTTTATGGTGTAGTTCGTGACGGTCCTGATGGAAGCT
|| ||| || | || ||| || || || | ||| |||| | ||| || | ||| | ||| | | | | || | |||||||| | ||||| ||||||||||| | | | | || ||| | |||||||||||||| || || || ||||| |||||||||| |||||||||||
-------------------------------------------------gtaaaatttcattcctttatta------tcaattgaa---tttaacatattgat----caacgtttaagtctagtat-----aattcttttact-----gcttttctgctgttgcagATAGAAGATTTTTGGAAAGAAGCCCTGTTATTGAGCTCATTGCATCATCCAAATGTTGTGTCGTTCTATGGGATAGTTCGTGATGGTCCTGATGGTTCTC
upper sequence: LOC_Os02g54510.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv11s0052g01480.t01 (Vitis vinifera), 3'ss of exon 3
gtatgcttgattgacttgttaacaccttagaacttttaggattgatttcatagctttttttttccttgttaaagatttctgttaaaaccctctggatagtgattttcttgcttttgtgtattctatggagaagatctctagttcagatatatatgtggttttgcagATTGCTGATTTCTGGAAAGAAGCTCAGATTCTAAGTTCACTTCATCATCCAAATGTGGTTTCATTTTATGGTGTAGTTCGTGACGGTCCTGATGGAAGCT
|| | |||| | ||| | ||| || | || | | || | ||||||| || | | || | || | || | || || |||||||| ||||||||||| || ||| ||| | |||||| | |||||||||||||| ||||| ||||||||| |||||||||| || |||| ||| |
-------------------------------------gagaataattttgcaacttcagtgttc--tgctgtagttcattaccaat----------------tacacttgcttcagtttgcatt--------gactgtttgtctatccatct---tgccgttacagATTGCGGATTTCTGGAAGGAGGCTTTGATATTGAGTTCATTACATCATCCAAATGTCGTTTCCTTTTATGGTATAGTTCGTGATGGCCCTGGTGGCTCTT
upper sequence: LOC_Os02g54510.3 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S66_220V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatgcttgattgacttgttaacaccttagaacttttaggattgatttcatagctttttttttccttgttaaagatttctgttaaaaccctctggatagtgattttcttgcttttgtgtattctatgga-gaagatctctagttcagatatatatgtggtt-ttgcagATTGCTGATTTCTGGAAAGAAGCTCAGATTCTAAGTTCACTTCATCATCCAAATGTGGTTTCATTTTATGGTGTAGTTCGTGACGGTCCTGATGGAAGCT
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----gtatgatagtcgggt--gtattctagtggatctctgatatatggcttaacttacaaattgaacgtctttgacttagggtctacctttacagagtgt-attcaaatgtataggtatatcgtttgcatgtacttctgtcagtaatgtggagttgtgtttgttgcagATTGCTGATTTTTGGAGAGAGGCATGCACATTGAGTCAGTTACATCATCCTAATGTGGTTGCCTTTTATGGAGTAGTTCGTGACGGTCCTGGAGGGACACMapped 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|29677568|gb|CB673843.1|CB673843EST: GGATAAAGGCTAGCTGTTTTGCTGGCAGACCATCTGAGAGAGAGCGTTTG ATTGCTGATTTCTGGAAAGAAGCTCAGATTCTAAGTTCACTTCATCATCCA
genomic: GGATAAAGGCTAGCTGTTTTGCTGGCAGACCATCTGAGAGAGAGCGTTTGgtatgcttga ... ggttttgcagATTGCTGATTTCTGGAAAGAAGCTCAGATTCTAAGTTCACTTCATCATCCA
EST:
gi|66924155|gb|CX111003.1|CX111003EST: GGATAAAGGCTAGCTGTTTTGCTGGCAGACCATCTGAGAGAGAGCGTTTG ATTGCTGATTTCTGGAAAGAAGCTCAGATTCTAAGTTCACTTCATCATCCA
genomic: GGATAAAGGCTAGCTGTTTTGCTGGCAGACCATCTGAGAGAGAGCGTTTGgtatgcttga ... ggttttgcagATTGCTGATTTCTGGAAAGAAGCTCAGATTCTAAGTTCACTTCATCATCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgtgtattctatggagaagatctctagttcagatatatatgtggttttgcagATTGCTGATTTCTGGAAAGAAGCTCAGATTCTAAGTTCACTTCATCATCCAAATGTGGTTTCATTTTATGGTGTAGTTCGTGACGGTCCTGATGGAAGCT
agatatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcttgattgacttgttaacaccttagaacttttaggattgatttcatagctttttttttccttgttaaagatttctgttaaaaccctctggatagtgattttcttgcttttgtgtattctatggagaagatctctagttcagatatatatgtggttttgcagATTGCTGATTTCTGGAAAGAAGCTCAGATTCTAAGTTCACTTCATCATCCAAATGTGGTTTCATTTTATGGTGTAGTTCGTGACGGTCCTGATGGAAGCT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG