Sequence
atgc intronic sequence ATGC exonic sequenceGTTCGATCGTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGTGATACAGgtatggttcatagctacctttcaagttaacgttttcattcttctctgctagcctttggagtggcgtgttgatgtttgatttgaggcgttctatatgtatc...
Basic information
species | Oryza sativa |
transcript | LOC_Os06g45840.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g45840.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G057408_T01 (Zea mays), 5'ss of exon 2
GTTCGATCGTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGTGATACAGgtatggttcatagctacc-----tttcaagttaacgttttcattcttctctgctagcct---ttggagtggcgtgttgatgtttgatttg-aggcgttctatatgtatc---------------
|| |||||||||||||| || ||||||||||| ||||||||||| ||||| ||||||||| | |||| | ||| | | | ||| ||| |||| ||| | | | || || | | || | |||| | | || || | | |
TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgta--atccataaccacccaaaatccttaatggtagttctcaaagttct-tgcgatcttcagttacaggcattcggtaataaatactttgtaatcattgtaaactttacaatgtcctttgatag
upper sequence: LOC_Os06g45840.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G170148_T01 (Zea mays), 5'ss of exon 2
GTTCGATCGTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGTGATACAGgtatggttcatagctacctt-----tcaagttaacgttttca---ttcttct---------ctgctagcctttgg-agtggcgtgttgatgtttgatttgaggcgttctatatgtatc---------------------------
|| |||||||||||||| |||||||||||||| || ||||| || ||||| ||||||||| | |||||| ||| | | | ||| ||| | ||||| || | || || || | || ||| | | || | | || || |
TTTTGATCGTGATTGGAAGAAGATTGAAGCATATGTCGGCTCGAAGACTGTTATACAGgta--atccatagccaccctaagtccttaacaatagttctcaaagtacttctgatcttaagctacaggcattcggtaatgattacttggtaatcaatctatgctgtataatgtccccaatctataaaaaaatgttcctttgacag
upper sequence: LOC_Os06g45840.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA09G24400.1 (Glycine max), 5'ss of exon 2
GTTCGATCGTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGTGATACAGgta----tggtt---catagctacctttcaagt-taacgttttcattcttctctgctagcctttggagtggcgtgttgatgtttgatttgaggcgttctatatgtatc
||| || ||||| ||||||||||||||||||| ||||| ||||| | ||| ||||||||| | || || | || || | | | || | | ||| | || | | | | || | ||| ||| |||| || | |
GTTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGTTATACAGgtaattctaattgaacaaaaaaactttctttgcctgaagtgcagaattatctttagta-tttctcaatttaagtctagatatttcattttagtctgctcct-------
upper sequence: LOC_Os06g45840.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA16G29740.1 (Glycine max), 5'ss of exon 2
GTTCGATCGTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGTGATACAGgtatggttcat------agctacctttca--agttaacgttttcattcttctctgctagcctttggagtggcgtgttgatgtttgatttgaggcgttctatatgtatc
||| |||||||||||||||||||||||||||| ||||| ||||| | ||| ||||||||| |||| | | ||||| | | || | | | ||| | | | | | | | || | ||| | | || || ||
GTTTGATCGTGATTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGTTATACAGgtaattctcattgaacaaaaaaactttctttgcctgaagtgtagaattatctttaatc-tttctcaatttgagtctagatctgcacctagaaagtatccat-------
upper sequence: LOC_Os06g45840.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ37776 (Selaginella moellendorffii), 5'ss of exon 2
GTTCGATCGTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGTGATACAGgtatggttcatagctacctttcaagttaacgttttcattcttctctgctagcctttggagtggcgtgttgatgtttgatttgaggcgttctatatgtatc
|||||||| |||||||| |||||||| || | ||| ||||| ||||| ||||||||||| | | | | ||| | | | | || ||||||
CTTCGATCGCGATTGGAAGAAGATTGAGGCCTTCGTGGGCTCTAAAACCGTGATACAGgtgagagttctctttgttttttctttctgtgatccttctttttgttgctag-------------------------------------------------
upper sequence: LOC_Os06g45840.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ32076 (Selaginella moellendorffii), 5'ss of exon 2
GTTCGATCGTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGTGATACAGgtatggttcatagctacctttcaagttaacgttttcattcttctctgctagcctttggagtggcgtgttgatgtttgatttgaggcgttctatatgtatc
|||||||| |||||||| |||||||| || | ||| ||||| ||||| ||||||||||| | | | ||| | | | | ||| ||||||
CTTCGATCGAGATTGGAAGAAGATTGAGGCCTTCGTGGGCTCTAAAACCGTGATACAGgtgagagctctctttgttttttctttctctgatccttcttttcgttgctag-------------------------------------------------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|33678202|gb|CF306441.1|CF306441EST: GTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGTGATACAG ATAAGGAGCCATGCACAAAAATACTTTTTGAAGGTTCAGAAAAATGGTACA
genomic: GTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGTGATACAGgtatggttca ... cttttgacagATAAGGAGCCATGCACAAAAATACTTTTTGAAGGTTCAGAAAAATGGTACA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTCGATCGTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGTGATACAGgtatggttcatagctacctttcaagttaacgttttcattcttctctgctagcctttggagtggcgtgttgatgtttgatttgaggcgttctatatgtatc
- - - - - - - - - - - TTGAAG
- - - - - - - - - - - - TGAAGC