Sequence
atgc intronic sequence ATGC exonic sequenceGCCAGAACCTCTCCCGAGGGAATTTCCCAAGGATGAGGATCAAAGCCTTGTGAAGAGGAACAAGAGGATGCTGGGGAAGCTTCTTGTCGGTACATTAGAGgtaaccgattcaatagacatacaaaggaacaatccatgggtcaagcgataataagatatcaacagttttcagtgtttcctctccaactgatacacacaaa...
Basic information
species | Oryza sativa |
transcript | LOC_Os03g49520.2 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g49520.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G102475_T03 (Zea mays), 5'ss of exon 5
GCCAGAACCTCTCCCGAGGGAATTTCCCAAGGATGAGGATCAAAGCCTTGTGAAGAGGAACAAGAGGATGCTGGGGAAGCTTCTTGTCGGTACATTAGAGgtaac-cgattcaatagacat--acaaaggaacaatccatgggtcaagcgataataagatatcaacagttttcagtgtttcctctccaactgatacacacaaa
|||||| || || ||||| |||||| | ||||||| | || | |||| ||||| ||||||||||||||| ||||||||||||||||||||||||||| | |||| | ||| | || | | | || || ||| || || | || | | | ||| | || || |
GCCAGAGCCAGCTCCAAGGGAGCTTCCCAGGAATGAGGACCCGAGTTTGGTGAGAAGGAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAGgtaaagcaattctctgcacactgatgaatctgtacttc-tgcaagaatgcatatcaacctaatgtgatagttaatttctatttctgcctctagtattcctt--
upper sequence: LOC_Os03g49520.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G810275_T02 (Zea mays), 5'ss of exon 5
GCCAGAACCTCTCCCGAGGGAATTTCCCAAGGATGAGGATCAAAGCCTTGTGAAGAGGAACAAGAGGATGCTGGGGAAGCTTCTTGTCGGTACATTAGAGgtaac-cgattcaatagacatacaaaggaacaat--ccatgggtcaagcgataataagatatcaacagttttcagtgtttcctctccaactgatacacacaaa
|||||| || || ||||| |||||| | ||||||| | | | |||| || || ||||||||||||||| ||||||||||||||||||||||||||| | |||| | | | | | | | | | | || || ||| | | || | ||| | |||| || | | | |
GCCAGAGCCAGCTCCAAGGGAGCTTCCCAGGAATGAGGACCCGAATTTGGTGAGAAGAAATAAGAGGATGCTGGGGCAGCTTCTTGTCGGTACATTAGAGgtaaagcaattctttgcata-atgatgaatctgtactcctgcaagaatacatattgacctaatgtggctgttctctatttctgtctcattccttggaaaaa--
upper sequence: LOC_Os03g49520.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G842421_T01 (Zea mays), 5'ss of exon 3
GCCAGAACCTCTCCCGAGGGAATTTCCCAAGGATGAGGATCAAAGCCTTGTGAAGAGGAACAAGAGGATGCTGGGGAAGCTTCTTGTCGGTACATTAGAGgtaac-cgattcaatagacatacaaaggaaca---atccatgggtcaagcgataataagatatca--acagttttcagtgtttcctctccaactgatacacacaaa-------------------------------------------------------
|||||| || || ||||| |||||| | ||||||| | || | |||| ||||| ||||||||| ||||| ||||||||||||||||||||||||||| | |||| | ||||| | ||| | || || ||| || || | |||| || || | || || || | ||
GCCAGAGCCAGCTCCAAGGGAGCTTCCCAGGAATGAGGACCCGAGTTTGGTGAGAAGGAATAAGAGGATGTTGGGGCAGCTTCTTGTCGGTACATTAGAGgtaaagcaattctctg--catactgatgaatctgtacttctgcaagaatgcatatcaacctaatgtgatagttaatttctatttctgccttgctcat-catagaagagctgcttgtaatcatgacatagtttgtattgtggtctgtttttcatctggccagMapped 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|29646297|gb|CB651304.1|CB651304EST: TGAAGAGGAACAAGAGGATGCTGGGGAAGCTTCTTGTCGGTACATTAGAG AAATTTCAGCAAGAGGACAAAAAACTGTCCAACACAGAGGCTTATATGCGC
genomic: TGAAGAGGAACAAGAGGATGCTGGGGAAGCTTCTTGTCGGTACATTAGAGgtaaccgatt ... ggtaatccagAAATTTCAGCAAGAGGACAAAAAACTGTCCAACACAGAGGCTTATATGCGC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCCAGAACCTCTCCCGAGGGAATTTCCCAAGGATGAGGATCAAAGCCTTGTGAAGAGGAACAAGAGGATGCTGGGGAAGCTTCTTGTCGGTACATTAGAGgtaaccgattcaatagacatacaaaggaacaatccatgggtcaagcgataataagatatcaacagttttcagtgtttcctctccaactgatacacacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctctcc