Sequence
atgc intronic sequence ATGC exonic sequence...tagttcatattgacatcatttgatgacaattaatgcaaatcatttatattctgtttgttaccttgttttctgactttaaatcatttcacaacttcaacagCTAGATATGGCGGAAGAGTGCCTTGTGCAAGCGAAGGACTTAAGTGGCCTGTTGCTACTATATTCATCTCTTGGAGATGCTGAGGGAATCGAGAAGCTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05180.4 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 4
tagttcatattgacatcatttgatgacaattaatgcaaatcatttatattctgtttgttacc--ttgttttctgactttaaatcatttcacaacttca----acagCTAGATATGGCGGAAGAGTGCCTTGTGCAAGCGAAGGACTTAAGTGGCCTGTTGCTACTATATTCATCTCTTGGAGATGCTGAGGGAATCGAGAAGCTTG
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-atgtcaaattgaga-catgacctaa-atcgaacatatcctatctgtatta-gctcgtgaatgatagccttttggcgt--gggtatgccacaactctacattgcagCTAGAGATGGCAGAGGAATGCCTTCTTCAAGCAAAGGACTTAAGTGGCTTGTTGCTACTGTACTCATCTCTTAGAGATGCTGAAGGAATTGAAAAGCTTG
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 18
-tagttcatattgacatcatttgatgacaattaatgcaaatcat-ttatattctgtttgttaccttgttttctgactttaaatcatttcacaacttcaacagCTAGATATGGCGGAAGAGTGCCTTGTGCAAGCGAAGGACTTAAGTGGCCTGTTGCTACTATATTCATCTCTTGGAGATGCTGAGGGAATCGAGAAGCTTG
|| || ||||| | | | || || | | | || || || || || ||| || || || ||| | | || | |||||||| |||||||| || |||||| | ||||||||||| ||||||||| |||||||| | || |||||||||||||||||||| ||||| || |||||||
gatgtcaattgagacatgacctaaatcgaacatatcctatctgtactagcttgtgaatgataacttattgg-tgtgggtatgccataactctaccttg-cagCTAGAGATGGCGGAGGAATGCCTTCTTCAAGCGAAGGATTTAAGTGGCTTGTTGCTATTGTACTCATCTCTTGGAGATGCTGAAGGAATTGAAAAGCTTG
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 19
tagttcatattgacatcatttgatgacaattaatgcaaatcatttatattctgtttgttacc--ttgttttctgactttaaatcatttcacaacttca----acagCTAGATATGGCGGAAGAGTGCCTTGTGCAAGCGAAGGACTTAAGTGGCCTGTTGCTACTATATTCATCTCTTGGAGATGCTGAGGGAATCGAGAAGCTTG
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-atgtcaaattgaga-catgacctaa-atcgaacatatcctatctgtatta-gctcgtgaatgataaccttttggcgt--gggtatgccacaactctacattgcagCTAGAGATGGCAGAGGAATGCCTTCTTCAAGCAAAGGACTTAAGTGGCTTGTTGCTACTGTACTCATCTCTTGGAGATGCTGAAGGAATTGAAAAGCTTG
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G448913_T01 (Zea mays), 3'ss of exon 8
---tagttcatattgacatcatttgatgacaattaatgcaaatcatttatattctgtttgttaccttgttttctgactttaaatcattt--cacaacttcaacagCTAGATATGGCGGAAGAGTGCCTTGTGCAAGCGAAGGACTTAAGTGGCCTGTTGCTACTATATTCATCTCTTGGAGATGCTGAGGGAATCGAGAAGCTTG
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atgcgaatgtgaatgatgtcaatttgagaca--tgacctaaatcgaacatatcctatctgta---ttagctcatgaatgatagccttttggcgtgggtatgccagCTAGAGATGGCAGAGGAATGCCTTCTTCAAGCAAAGGACTTAAGTGGCTTGTTGCTACTGTACTCATCTCTTGGAGATGCTGAAGGAATTGAAAAGCTTGMapped 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|2443004|gb|C74775.1|C74775EST: GTGAATCTAAGTGGAAGCAGTTNGGTGAACTGGCTATGTCCACAGGCAAG CTAGATATGGCGGAN-AGTGCCTTGTGCAAGCGAAGGACTTAA
genomic: GTGAATCTAAGTGGAAGCAGTTGGGTGAACTGGCTATGTCCACAGGCAAGgttagttcat ... acttcaacagCTAGATATGGCGGAAGAGTGCCTTGTGCAAGCGAAGGACTTAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattctgtttgttaccttgttttctgactttaaatcatttcacaacttcaacagCTAGATATGGCGGAAGAGTGCCTTGTGCAAGCGAAGGACTTAAGTGGCCTGTTGCTACTATATTCATCTCTTGGAGATGCTGAGGGAATCGAGAAGCTTG
ttctgac putative branch site (score: 2)
actttaaatcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagttcatattgacatcatttgatgacaattaatgcaaatcatttatattctgtttgttaccttgttttctgactttaaatcatttcacaacttcaacagCTAGATATGGCGGAAGAGTGCCTTGTGCAAGCGAAGGACTTAAGTGGCCTGTTGCTACTATATTCATCTCTTGGAGATGCTGAGGGAATCGAGAAGCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - -ttgatga
- - - - - - - - - - - - - - - taatgca
- - - - - - - - - - - - - - - - - - - - - - - - - ctgtttg