Sequence
atgc intronic sequence ATGC exonic sequence...gttctggcaaattagctcttcttggttccctttttacggaattgaaagcatggccatgattgtacatctaccaactaatttattatttattgattgccagTTGGGTATTATTATTTCTTTTCAAGACAAGTTTTGAGGAGCGTGATCTATGGGGATCAACCAAGAAATAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g50170.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g50170.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G406177_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------------------gttctggcaaattagct-cttcttggttccctttttacggaat---tgaaagcatggccatgattgtacat-ctaccaactaattt---------attatttattgattgccagTTGGGTATTATTATTTCTTTTCAAGACAAGTTTTGAGGAGCGTGATCTATGGGGATCAACCAAGAAATAG
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gtgtgtgataagagatttagttttatcttggaatatagtggttacatattgtttacctctttcctgggtatttttctccaaaccttttcttggtaaacaatttgcttccgtataggcttttgatagatggtgttcaaatatgatcggcataacatgttctaacaactaacatttataccccattttttgtttgtttccagTTGGGTACTACTATTTCTTTTCAAGACATGTTATTAGAAGTGTAATCTATGGAGAACAACCAAGAAATAG
upper sequence: LOC_Os05g50170.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G437845_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------------------gttctggcaaa---ttagctct--tcttggttccctttttacggaattgaaagcatggccatgattgtacat-ctaccaactaa--tttat-------tatttattgattgccagTTGGGTATTATTATTTCTTTTCAAGACAAGTTTTGAGGAGCGTGATCTATGGGGATCAACCAAGAAATAG
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gtgtgtgataagagatttagttttatcttggaatatagtggttacatattctttacctctttcctgggtatttttctgcaaacattttcctgataaacagtttgcttccgtataggcttctgatagatggtgttcaaa-tatgatcggcataacatgttctaacaactaacatttatacccccttttttgtttgtttccagTTGGGTACTACTATTTCTTTTCAAGACATGTTATTAGAAGTGTAATCTATGGAGAACAACCAAGAAATAG
upper sequence: LOC_Os05g50170.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G427351_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------------------------------------------------gttctggcaaa---ttagctct--tcttggttccctttttacggaattgaaagcatggccatgattgtacat-ctaccaactaa--tttat-------tatttattgattgccagTTGGGTATTATTATTTCTTTTCAAGACAAGTTTTGAGGAGCGTGATCTATGGGGATCAACCAAGAAATAG
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gtgtgtggtaagagatttagttttatcttggaatatagtggttacatattctttacctctttcctgggtatttttctccaaaccttttcctggtaaacagtttgcttccgtataggcttctgatagatggtgttcaaa-tatgatcggcataacatgttctaacaactaacatttatacccccttttttgtttgtttccagTTGGGTACTACTATTTCTTTTCAAGACATGTTATTAGAAGTGTAATCTATGGAGAACAACCAAGAAATAG
upper sequence: LOC_Os05g50170.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G854930_T01 (Zea mays), 3'ss of exon 3
--------------------------------------------------------------------------------------gttctggcaaa---ttagctct--tcttggttccctttttacggaattgaaagcatggccatgattgtacat-ctaccaactaa--tttat-------tatttattgattgccagTTGGGTATTATTATTTCTTTTCAAGACAAGTTTTGAGGAGCGTGATCTATGGGGATCAACCAAGAAATAG
| |||| ||| || ||| | | || | | | | || || ||| ||| | || | | ||| ||||||| ||||| | ||| || || | ||||||||| || ||||||||||||||||| ||| | || || || |||||||| || ||||||||||||||
gtgtgtgataagagatttagttttatcttggaatatagtggttacatattctttacctctttcctgggtatttttctccaaaccttttcctggtaaacagtttgcttccgtataggcttctgatagatggtgttcaaa-tatgatcggcataacatgttctaacaactaacatttatacccccttttttgtttgtttctagTTGGGTACTACTATTTCTTTTCAAGACATGTTATTAGAAGTGTAATCTATGGAGAACAACCAAGAAATAGMapped 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|88415590|gb|CI589182.1|CI589182EST: CGCTGCCCTCATAATATATGCAATTTTACTTATGCCCGGTTTCATAAGAG TTGGGTATTATTATT
genomic: CGCTGCCCTCATAATATATGCAATTTTACTTATGCCCGGTTTCATAAGAGgtagataaaa ... tgattgccagTTGGGTATTATTATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagcatggccatgattgtacatctaccaactaatttattatttattgattgccagTTGGGTATTATTATTTCTTTTCAAGACAAGTTTTGAGGAGCGTGATCTATGGGGATCAACCAAGAAATAG
taccaactaatttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttctggcaaattagctcttcttggttccctttttacggaattgaaagcatggccatgattgtacatctaccaactaatttattatttattgattgccagTTGGGTATTATTATTTCTTTTCAAGACAAGTTTTGAGGAGCGTGATCTATGGGGATCAACCAAGAAATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
-ttctggc
- - - - - - - - -cttcttg
- - - - - - - - - - - - - - - - - - - - - - - - catggcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgattgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catctac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caactaa