Sequence
atgc intronic sequence ATGC exonic sequencegtttgtcttttccattgcatactcatcatagtcttccccttcattattgtaaataaaataccttttttttccagAGGAACAAAGCTCCCAATGAGCAAGGAATTCCCTTGCTGATGCCTCATCACCACATGGTAATTCCACATTACAAGGGCATAGGCCAAGAAATTAATAGTG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g29050.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 10
gtttgtcttttccattgcatactcatcatagtcttccccttcattattgtaaataaaataccttttttt--tccagAGGAACAAAGCTCCCAATGAGCAAGGAATTCCCTTGCTGATGCCTCATCACCACATGGTAATTCCACATTACAAGGGCATAGGCCAAGAAATTAATAGTG
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---------gttgcttatatccttgtggtctgcttatcatagaaagcggtaaactaattgtttttttttctttcagAGGAACAAAGCTCTAAATGAGCAAGCAATTCCCTTACTGATGCCTCATTACCACATGGTAATTCCACACTACAAGGGTAGAAGCAAAGAAACAAATGATG
upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 11
---------gtttgtcttttccattgcatact-----catcatagtcttccccttcattattgtaaata--aaataccttttttttc--------cagAGGAACAAAGCTCCCAATGAGCAAGGAATTCCCTTGCTGATGCCTCATCACCACATGGTAATTCCACATTACAAGGGCATAGGCCAAGAAATTAATAGTG
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gttagtcttattttgcaattgcattgaagtcttggagcattctggtcctattcctatattccctaaataggaaataatattttttttattaacgtcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG
upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 11
----------------gtttgtctt----ttccattgcatactcatcatagtcttccccttc-attattgtaaataaaatacctttttttt---ccagAGGAACAAAGCTCCCAATGAGCAAGGAATTCCCTTGCTGATGCCTCATCACCACATGGTAATTCCACATTACAAGGGCATAGGCCAAGAAATTAATAGTG
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gttagtcttattttgcagttgcattgaagtcttgaagcattctggtcctattcctatattcccaaaataggaaataatattttttttattaacatcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG
upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 3'ss of exon 12
gtttgtcttttccattgcatactcatcatagtcttccccttcattattgtaaataaaatacctt-------------ttttttccagAGGAACAAAGCTCCCAATGAGCAAGGAATTCCCTTGCTGATGCCTCATCACCACATGGTAATTCCACATTACAAGGGCATAGGCCAAGAAATTAATAGTG
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-gttgatgtcttcactacatactccctagttcttctttcaaaagtataataaaccttttatctcaatacaagcatacttttctgcagAGAAATAAAGCTCCAAATGAGCAAGCAATTCCACTACTTATGCCTCAGCAGCACATGGTCATTCCACATTACATGGGAAGGAGCAGAGAGATGGAGGTTGMapped 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|58669537|gb|CK058223.1|CK058223EST: CTTGTCGGGATGTTGCAAGGCATTTTGTTCAGCGCTGGAATTATGCAAAG AGGAACAAAGCTCCCAATGAGCAAGGAATTCCCTTGCTGATGCCTCATCAC
genomic: CTTGTCGGGATGTTGCAAGGCATTTTGTTCAGCGCTGGAATTATGCAAAGgtttgtcttt ... ttttttccagAGGAACAAAGCTCCCAATGAGCAAGGAATTCCCTTGCTGATGCCTCATCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactcatcatagtcttccccttcattattgtaaataaaataccttttttttccagAGGAACAAAGCTCCCAATGAGCAAGGAATTCCCTTGCTGATGCCTCATCACCACATGGTAATTCCACATTACAAGGGCATAGGCCAAGAAATTAATAGTG
taccttttttttcc CT-rich tract
ttcattattgtaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtcttttccattgcatactcatcatagtcttccccttcattattgtaaataaaataccttttttttccagAGGAACAAAGCTCCCAATGAGCAAGGAATTCCCTTGCTGATGCCTCATCACCACATGGTAATTCCACATTACAAGGGCATAGGCCAAGAAATTAATAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA