Sequence
atgc intronic sequence ATGC exonic sequence...cactgaccctaatttgcacttgcattgactgataaatgaagctagctgtgtagttttcttgatattgattattttgtcttttgctacaaatttgctttagATTGATGACATGGATAGACTTATTGAGATAGTAAAGCAAGCAGCAAAAGAAGGAGCACTGGTTTTATATACTCTTGCTGATCCTTCAATGGCTGAGGCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os07g34640.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g34640.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G004880_T01 (Zea mays), 3'ss of exon 1
cactgaccctaatttgcacttgcattgactgataaatgaagctagctgtgta--gttttcttgatatt-gattat-tttgtcttttgctaca---------aatttgctttagATTGATGACATGGATAGACTTATTGAGATAGTAAAGCAAGCAGCAAAAGAAGGAGCACTGGTTTTATATACTCTTGCTGATCCTTCAATGGCTGAGGCAA
||| ||||| ||| || | || | | |||||| | ||| ||| |||| | | | ||| | | ||| ||| | || ||||||||| |||||||| ||||| ||||| || |||||||||||||||| ||||| ||||||||| ||||||| |||||||||||||||||||||||| |||
-----------ttttatacttgtgttggct--tgaaaaatgttagctgcacatcacttttttggtattaggctgcatctgttgtaagtaacagcttctgataatgttctgtagATTGATAACATGGATCGACTTCTTGAGGTAATAAAGCAAGCAGCAAAGGAAGGGGCACTGGTTCTATATACCCTTGCTGATCCTTCAATGGCTGAGTCAA
upper sequence: LOC_Os07g34640.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G131286_T01 (Zea mays), 3'ss of exon 1
cactgaccctaatttgcacttgcatt---gactgataaatgaagctagctgtgtagttttcttgatattgattattttgtcttttgctacaaatttgctttagATTGATGACATGGATAGACTTATTGAGATAGTAAAGCAAGCAGCAAAAGAAGGAGCACTGGTTTTATATACTCTTGCTGATCCTTCAATGGCTGAGGCAA
|| || ||||| | |||| ||| ||| | || || ||| || || || || | || || | ||| | || |||||||| ||||||||| ||||||||||| || |||||||||||||||| ||||| ||||||||| | || || ||||| |||||||||||||| ||||| |
tacggatgg-aatttatatccacatttctacttgaaaaacgtcactttttg-gtaaggggctgcatcttttgtaagtaacagctt-ctgctaatgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAAGGGGCACTGGTTCTCTACACCCTTGCCGATCCTTCAATGGCCGAGGCGA
upper sequence: LOC_Os07g34640.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv10s0116g00390.t01 (Vitis vinifera), 3'ss of exon 1
cactgaccctaatttgcacttgcattgactgataaatgaagctagctgtgtagttttcttgatattgattattttgtcttttgctacaaatt-tgctt--tagATTGATGACATGGATAGACTTATTGAGATAGTAAAGCAAGCAGCAAAAGAAGGAGCACTGGTTTTATATACTCTTGCTGATCCTTCAATGGCTGAGGCAA
| || || | | | | || | || || ||| | | | || ||||| | | ||| | | ||||| ||||||||||| || | | |||||||||||||||||||| |||||||| ||| || || | || ||| | ||||| |||||||||||||| |
-attggattctgtt-gta-tagagctgccggagttttggtcttagaactcttgcattaaaatggatgatttgagtatatttgatggtcatctatgcttgttagATTGATGATGCAGAGCCGTTGGTGGAGATAGTAAAGCAAGCAGCTAAAGAAGGTGCAATGCTTGTTTACACTTTAGCTGACCCTTCAATGGCTGAATCTGMapped 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|29661235|gb|CB657510.1|CB657510EST: ACTGCCTCGTCGACCGCGGCTGCGCCGTCAACACACACCTCTTCAACGGG ATTGATGACATGGATAGACTTATTGAGATAGTAAAGCAAGCAGCAAAAGAA
genomic: ACTGCCTCGTCGACCGCGGCTGCGCCGTCAACACACACCTCTTCAACGGGgtaaagatcc ... tttgctttagATTGATGACATGGATAGACTTATTGAGATAGTAAAGCAAGCAGCAAAAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtgtagttttcttgatattgattattttgtcttttgctacaaatttgctttagATTGATGACATGGATAGACTTATTGAGATAGTAAAGCAAGCAGCAAAAGAAGGAGCACTGGTTTTATATACTCTTGCTGATCCTTCAATGGCTGAGGCAA
tattgat putative branch site (score: 3)
tttgcttt putative PPT
ttttcttgatattgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cactgaccctaatttgcacttgcattgactgataaatgaagctagctgtgtagttttcttgatattgattattttgtcttttgctacaaatttgctttagATTGATGACATGGATAGACTTATTGAGATAGTAAAGCAAGCAGCAAAAGAAGGAGCACTGGTTTTATATACTCTTGCTGATCCTTCAATGGCTGAGGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - -acttgca
- - - - - - - - - - - - ttgactg
- - - - - - - - - - - - - - - - -aaatgaag
- - - - - - - - - - - - - - - - - - - - -ctagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - tttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctacaaa