Sequence
atgc intronic sequence ATGC exonic sequence...gtgctgttgatcggttcacgatgaacgaagctgacagtgaacaatcgtgcctgaagttctgaacagttgacgaagtttaattaactttttacgcgtgcagAGAGATCATGCACGCGATGTGGAAGCCGCAGAAGTTCAAGTACATCTACCTGGTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCC
Basic information
species | Oryza sativa |
transcript | LOC_Os05g37470.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g37470.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G067022_T02 (Zea mays), 3'ss of exon 5
---gtgctgttgatcggttcacgatgaacgaagctgacagtgaacaatcgtgcctgaagttctgaacagttgacgaagtttaattaactttttacgcgtgcagAGAGATCATGCACGCGATGTGGAAGCCGCAGAAGTTCAAGTACATCTACCTGGTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCC
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cgtgaaggactctccttttttttatcagcatatactctatgtctctatctcattttctattttaaatttctcactgatttc---tgatgccccgcgcgcgcagGGAGATCATGCACGCGATGTGGAAGCCTCGCAAGTTCAAGTACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTTCCGTCGGCGGCGGCC
upper sequence: LOC_Os05g37470.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S213_89V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------gtgctgttgatcggttcacgatgaacgaagctg--acagtgaacaatcgtgc-ctgaagttctgaacagttgacgaagtttaa-ttaactttttacgcgtgc-agAGAGATCATGCACGCGATGTGGAAGCCGCAGAAGTTCAAGTACATCTACCTGGTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCC
| | |||| | | |||| | | | | || | || | |||| | || || | | | || | || |||| ||| || |||||||||||||| |||| || || |||||||||||| | | |||| |||||||||||||||||||||||||||| | || || || |||
gtaagtaaaaaagggagctcctcctcctgctcctctctcaacggttttcatcccaatcgttcctcgatttttgttccagcaattttgtattgtcactcactgaggctcagagagaaaaaaggccctcaaacttcctaattactattgccagGGAGATCATGCACGCCATGTACAAACCCAGCAAGTTCAAGTACGTTTTCCTGTTGGCGACGCTGTACGTGTTCACGCTGACAATCCCCTCCGCAGTGGCA
upper sequence: LOC_Os05g37470.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ34222 (Selaginella moellendorffii), 3'ss of exon 5
gtgctgttgatcggttcacgatgaacgaagctgacagtgaacaatcgtgcctgaagttctgaacagttgacgaagtttaattaactttttacgcgtgcagAGAGATCATGCACGCGATGTGGAAGCCGCAGAAGTTCAAGTACATCTACCTGGTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCC
||||| | | | ||| | | || | | | | | | || |||||| | ||| |||||||||||||||||||||||||| || |||||||||| |||| || || || || | ||||| ||||| |||| || ||||| || ||||
-------------------------gtaagctttcgct--tctttcgctgttcttgcatggatcgataggcatcttctcataaactttg-atcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
upper sequence: LOC_Os05g37470.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
gtgctgttgatcggttcacgatgaacgaagctgacagtgaacaatcgtgcctgaagttctgaaca--gttgacgaagtttaat-taactttttacgcgtgcagAGAGATCATGCACGCGATGTGGAAGCCGCAGAAGTTCAAGTACATCTACCTGGTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCC
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--------------------gtaagctttcgcttctttcgctgttcttgcatggatcgataggctatgttgtcatcttttctcataaactttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCAMapped 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|29638464|gb|CB643473.1|CB643473EST: ACTGGCGCCACCAACATCCTCTACACTTTCGGCGGACACGCCGTCACTGT AGAGATCATGCACGCGATGTGGAAGCCGCAGAAGTTCAAGTACATCTACCT
genomic: ACTGGCGCCACCAACATCCTCTACACTTTCGGCGGACACGCCGTCACTGTgtaagtgcac ... acgcgtgcagAGAGATCATGCACGCGATGTGGAAGCCGCAGAAGTTCAAGTACATCTACCT
EST:
gi|86891273|gb|CI307993.1|CI307993EST: ACTGGCGCCACCAACATCCTCTACACTTTCGGCGGACACGCCGTCACTGT AGAGATCATGCACGCGATGTGGAAGCCGCAGAAGTTCAAGTACATCTACCT
genomic: ACTGGCGCCACCAACATCCTCTACACTTTCGGCGGACACGCCGTCACTGTgtaagtgcac ... acgcgtgcagAGAGATCATGCACGCGATGTGGAAGCCGCAGAAGTTCAAGTACATCTACCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgtgcctgaagttctgaacagttgacgaagtttaattaactttttacgcgtgcagAGAGATCATGCACGCGATGTGGAAGCCGCAGAAGTTCAAGTACATCTACCTGGTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCC
aattaac putative branch site (score: 2)
ctttttac CT-rich tract
aagtttaattaacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctgttgatcggttcacgatgaacgaagctgacagtgaacaatcgtgcctgaagttctgaacagttgacgaagtttaattaactttttacgcgtgcagAGAGATCATGCACGCGATGTGGAAGCCGCAGAAGTTCAAGTACATCTACCTGGTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG