Sequence
atgc intronic sequence ATGC exonic sequencegtttgatctttgagcaactttgccagcgctttttatatcctcctggacttcctttgttcttgttgttgtatcatccaatgctccttgcttatacagCCAACAGAAAGACACTTGCGGGTCAGAGAATATGTGACTCCTGAGAAGTTTGATTTCTGGAAGGAGTATGGGGAATCTCTGGGTTTTCTTTATGTTGCTA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g43576.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g43576.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G42600.1 (Glycine max), 3'ss of exon 7
gtttgatctttgagcaactttgccagcgctttttatatcctcctggacttcctttgtt-cttgt----tgttgtatcatccaatgctccttgcttatacagCCAACAGAAAGACACTTGCGGGTCAGAGAATATGTGACTCCTGAGAAGTTTGATTTCTGGAAGGAGTATGGGGAATCTCTGGGTTTTCTTTATGTTGCTA
||| | | | ||| | | | || | | || ||| | ||||| | |||| | || ||| || | | |||||||| ||||| |||| ||| ||||| |||||||||||||||| ||||||||| || || ||||||||| | |||||| |||||| ||||
gttggctaagcggacaatagttataatacaccttgcagatctttattattgatttttaacttgtggcttattgt-taattcaaaagattttattgttgcagCCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTTGCTTTCTGGAAAGAATACGGGGAATCTATTGGTTTTTGTTATGTAGCTA
upper sequence: LOC_Os05g43576.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA20G24430.1 (Glycine max), 3'ss of exon 5
gtttgatctttgagcaactttgccagcg--ctttttatatcctcctggact-tcctttgttcttg--ttgttgtatcatccaatgctccttgcttatacagCCAACAGAAAGACACTTGCGGGTCAGAGAATATGTGACTCCTGAGAAGTTTGATTTCTGGAAGGAGTATGGGGAATCTCTGGGTTTTCTTTATGTTGCTA
||||| || || | | | || | || | | || ||| | || || |||| | || | | || | | |||||||| ||||| |||| ||| ||||| |||||||||||||||||||||||||| || |||||||||||| | ||||||| ||| || ||||
gtttgctcagctgataatagtcataatagaccttgcaggtctttattattgatcgtttacttgtggcttattgt-taattcgaaagattttattgttgcagCCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTTGATTTCTGGAAAGAATATGGGGAATCTATTGGTTTTCGTTACGTAGCTA
upper sequence: LOC_Os05g43576.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv10s0071g01020.t01 (Vitis vinifera), 3'ss of exon 5
----gtttgatctttga--gcaacttt-gccagcgctttttatatcctcctggacttcctttgttcttgttgttgtatcatccaatgctccttgcttatacagCCAACAGAAAGACACTTGCGGGTCAGAGAATATGTGACTCCTGAGAAGTTTGATTTCTGGAAGGAGTATGGGGAATCTCTGGGTTTTCTTTATGTTGCTA
| ||| | ||| | | | || ||| | | | || | ||| | || | | ||| | | | || | | | | |||||||| | |||| | |||| ||| ||||| || ||||||||||||| |||||||||||| |||||||| || | || || | |||||||||||
ataagaggcatccacaaaagcagcctcagacaacgcacatcaa--ctaacttcagttcaagtttttaaacagatctattaataagtacttat-gttgctgcagCCAACTCCATTACACCTTACTGTCAAAGAGTATGTTACCCCTGAGAAGTTTGCTTTCTGGAAGGAATATGGGGAGTCAATTGGATTCCGTTATGTTGCTAMapped 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|88906312|gb|CI375384.1|CI375384EST: ATTTGAGGGCCATTGACGTTGATATTCTGACCTTGGGACAATATTTACAG CCAACAGAAAGACACTTGCGGGTCAGAGAATATGTGACTCCTGAGAAGTTT
genomic: ATTTGAGGGCCATTGACGTTGATATTCTGACCTTGGGACAATATTTACAGgtttgatctt ... gcttatacagCCAACAGAAAGACACTTGCGGGTCAGAGAATATGTGACTCCTGAGAAGTTT
EST:
gi|88247674|gb|CI247523.1|CI247523EST: ATTTGAGGGCCATTGACGTTGATATTCTGACCTTGGGACAATATTTACAG CCAACAGAAAGACACTTGCGGGTCAGAGAATATGTGACTCCTGAGAAGTTT
genomic: ATTTGAGGGCCATTGACGTTGATATTCTGACCTTGGGACAATATTTACAGgtttgatctt ... gcttatacagCCAACAGAAAGACACTTGCGGGTCAGAGAATATGTGACTCCTGAGAAGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctggacttcctttgttcttgttgttgtatcatccaatgctccttgcttatacagCCAACAGAAAGACACTTGCGGGTCAGAGAATATGTGACTCCTGAGAAGTTTGATTTCTGGAAGGAGTATGGGGAATCTCTGGGTTTTCTTTATGTTGCTA
ctccttgctt CT-rich tract
ttataca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgatctttgagcaactttgccagcgctttttatatcctcctggacttcctttgttcttgttgttgtatcatccaatgctccttgcttatacagCCAACAGAAAGACACTTGCGGGTCAGAGAATATGTGACTCCTGAGAAGTTTGATTTCTGGAAGGAGTATGGGGAATCTCTGGGTTTTCTTTATGTTGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG