Sequence
atgc intronic sequence ATGC exonic sequencegtatggtaacatatattcccaatgtgtgcattttttttaaatgattcttgtcagtcatgcattacttttctaagataagatgatgtacttgctgatatttttattaaatctttttagcctaactacattttttttttaaaaaaaattcaaacagCTAGGGTATTTGCTTTTCTGTCTGGTGCTCCTGATTATGGAGATGGTCAACTAGACACTAGGAGATATGGTGAACAATATGCTAGCAAAGGGGAAGACCC
Basic information
species | Oryza sativa |
transcript | LOC_Os05g37120.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g37120.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G141735_T01 (Zea mays), 3'ss of exon 5
gtatggtaacatatattcccaatgtgtgcattttttttaaatgattcttgtcagtcatgca-ttacttttctaag--ataagatgatgtac--ttgctgatatttttatta--aatcttttta-gcctaactacattttttttttaaaaaaaattcaaacagCTAGGGTATTTGCTTTTCTGTCTGGTGCTCCTGATTATGGAGATGGTCAACTAGACACTAGGAGATATGGTGAACAATATGCTAGCAAAGGGGAAGACCC
||| | |||| | |||| | | | | | || | || || ||| ||| ||| || ||| ||||||| |||| |||| | | | | | | | | | || || ||| | | | || | | | | ||||| ||||||||||||||||||||||||||||||||||||||| |||| ||||| || ||||||||||| || ||||||||||| ||||||| |||| |
gtaggtgaacacactttccata---------tctcatgagatatctggtgccattcaggcaattagcttcataactcgtaagatgctgtatctttgcaaacaacctagtaaccagtatctctatgcgtaattttttaatgttccttgtcatatggagagcagCTCGGGTATTTGCTTTTCTGTCTGGTGCTCCTGATTATGGAGCTGGTGTGCTAGATACCAGGAGATATGGGGAGCAATATGCTAGTAAAGGGGTAGACGC
upper sequence: LOC_Os05g37120.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G106140_T01 (Zea mays), 3'ss of exon 5
gtatggtaacatatattcccaatgtgtgcattttttttaaatgattcttgtcagtcatgca-ttacttttctaag--ataagatgatgtac---------ttgctgatatttttatta--aatctttttagcctaactacattttttttttaaaaaaaattcaaacagCTAGGGTATTTGCTTTTCTGTCTGGTGCTCCTGATTATGGAGATGGTCAACTAGACACTAGGAGATATGGTGAACAATATGCTAGCAAAGGGGAAGACCC
|| | | | | | || | | | |||| | ||||| ||| ||| || || ||| ||||||||||||| |||| | | | | | | | | | |||| |||| | |||| || | | | | ||||| | ||||||||||||||||||||||||||||||||||||| ||||| ||||| || ||||||||||| || ||||||||||| ||||||| |||| |
--gtgagtggacacactttccata-------tctcatgaaatatctggtgtcaatcaggcaactagcttaataactcataagatgatgtatgtttacactttgcaaacaatctagtaaccagtatctttatgctaatttacttttgttccttgtcatatggagagcagCTCGAGTATTTGCTTTTCTGTCTGGTGCTCCTGATTATGGAGCTGGTCTGCTAGATACCAGGAGATATGGGGAGCAATATGCTAGTAAAGGGGTAGACGC
upper sequence: LOC_Os05g37120.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G18930.1 (Glycine max), 3'ss of exon 5
gtatggtaacatatattcccaatgtgtgcattttttttaaatgattcttgtcagtcatgcattacttttctaagataagatgatgtacttgctgatatttttattaaatctttttagcctaactacattttttttttaaaaaaaattcaaacagCTAGGGTATTTGCTTTTCTGTCTGGTGCTCCTGATTATGGAGATGGTCAACTAGACACTAGGAGATATGGTGAACAATATGCTAGCAAAGGGGAAGACCC
|| || || | | ||| | || ||| |||| | |||||||| | || |||| |||| | || || ||| || ||| || | || || ||| || | || | ||||||| || ||||| || |||||||| | ||||||||||||| ||| ||| | ||||| || ||||||||||||||||||| |||||||| || || |
gtttg--aatgaacaaatacaaaacttacagttt------atgacttttgtcagt---gtgtttcttt-------------aatgttcaatcttccatacttaaagaagctt-------caagcagatgttatttctattgagaact---gcagCTAGAGTCTTTGCCTTCTTGTCTGGTCCCCCTGATTATGGAGCTGGACAATTGGACACGAGACGATATGGTGAACAATATGCAAGCAAAGGAGAGGATGC
upper sequence: LOC_Os05g37120.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G09540.1 (Glycine max), 3'ss of exon 5
gtatggtaacatatattcccaatgtgtgcattttttttaaatgattcttgtcagtcatgcattacttttctaagataagatgatgtacttgctgatatttttattaaatctttttagcctaactacattttttttttaaaaaaaattcaaacagCTAGGGTATTTGCTTTTCTGTCTGGTGCTCCTGATTATGGAGATGGTCAACTAGACACTAGGAGATATGGTGAACAATATGCTAGCAAAGGGGAAGACCC
|| || |||| | | ||| | || ||| |||| | |||| ||| | || |||| |||| | || || ||| || ||| || | || || ||| || | || | ||||||| || ||||| || |||||||| | ||||||||||||| ||| ||| | ||||| || ||||||||||||||||||| |||||||| || || |
gtttg--aacaaacaaatacaaaacttacagttt------atgacttttgttagt---gtgtttcttt-------------aatgttcaatcttcgatacttaaagaagctt-------caagcagatattatttctattgagaact---gcagCTAGAGTCTTTGCCTTCTTGTCTGGTCCCCCTGATTATGGAGCTGGACAATTGGACACAAGACGATATGGTGAACAATATGCAAGCAAAGGAGAGGATGC
upper sequence: LOC_Os05g37120.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G27460.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatggtaacatatattcccaatgtgtgcattttttttaaatgattcttgtcagtcatgcattacttttctaagataagatgatgtacttgctgatatttttattaaatctttttagcctaactacattttttttttaaaaaaaattcaa-acagCTAGGGTATTTGCTTTTCTGTCTGGTGCTCCTGATTATGGAGATGGTCAACTAGACACTAGGAGATATGGTGAACAATATGCTAGCAAAGGGGAAGACCC
| | | || | || | | || || || ||| | | || | | ||| ||| |||| || | | | | |||||||||| |||||||| || |||||| |||||||||||||| ||| ||| | || || || |||||||||||||||||||| || ||| ||| ||| |
--------------------------------------------------------gtatgtgaaattatttag-catgcccatactctat---atgtttcaacatagtcgtagtggccagttggtattgttttattgacttgatataagtgcagCTAGGGTGTTTGCTTTCCTATCTGGTCCTCCTGATTATGGACGTGGACAATTGGATACAAGTAGATATGGTGAACAATATGCAAGTAAAAGGGTAGATGC
upper sequence: LOC_Os05g37120.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0080g00510.t01 (Vitis vinifera), 3'ss of exon 5
gtatggtaacatata--------ttcccaatgtgtgcattttttttaaatgattcttgtcagtcatgcattactt---ttctaagataagatgatgtacttgctgatatttttattaaatctttttagcctaa-ctacattttttttttaaaaaaaattcaaacagCTAGGGTATTTGCTTTTCTGTCTGGTGCTCCTGATTATGGAGATGGTCAACTAGACACTAGGAGATATGGTGAACAATATGCTAGCAAAGGGGAAGACCC
|| || ||| | | ||| || ||||| || || ||| || | | | ||| || | | | | | | || ||||||| || | || | || | |||||| || |||| | ||||| |||||||||| ||||| ||| |||||||| ||||||| ||||||| ||| |||||||| || || | |||||||| ||||||||||| ||||| || || |
gtgtgataatgttcaaagctcatcaccctatttgtgctcagttcttgtgcaattaatggctccgctttaactcttaaatttcattttttcactttttcacttttgttattttttgtacactttctaaggacattctacatgttattttcattgaaaataagtgcagCTAGGGTCTTTGCCTTTTTGTCTGGTCCTCCTGACTATGGAGCTGGCCAACTAGATACAAGACGGTATGGTGAGCAATATGCTAGTAAAGGTGAGGATGCMapped 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|33675080|gb|CF303319.1|CF303319EST: TGCTCTAACTGACTACCTAAGTTCAGAGTATGGAACTACTTTTGCTTTGG CTAGGGTATTTGCTTTTCTGTCTGGTGCTCCTGATTATGGAGATGGTCAAC
genomic: TGCTCTAACTGACTACCTAAGTTCAGAGTATGGAACTACTTTTGCTTTGGgtatggtaac ... attcaaacagCTAGGGTATTTGCTTTTCTGTCTGGTGCTCCTGATTATGGAGATGGTCAAC
EST:
gi|29674495|gb|CB670770.1|CB670770EST: TGCTCTAACTGACTACCTAAGTTCAGAGTATGGAACTACTTTTGCTTTGG CTAGGGTATTTGCTTTTCTGTCTGGTGCTCCTGATTATGGAGATGGTCAAC
genomic: TGCTCTAACTGACTACCTAAGTTCAGAGTATGGAACTACTTTTGCTTTGGgtatggtaac ... attcaaacagCTAGGGTATTTGCTTTTCTGTCTGGTGCTCCTGATTATGGAGATGGTCAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttattaaatctttttagcctaactacattttttttttaaaaaaaattcaaacagCTAGGGTATTTGCTTTTCTGTCTGGTGCTCCTGATTATGGAGATGGTCAACTAGACACTAGGAGATATGGTGAACAATATGCTAGCAAAGGGGAAGACCC
gcctaac putative branch site (score: 2)
tttttagcctaactac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggtaacatatattcccaatgtgtgcattttttttaaatgattcttgtcagtcatgcattacttttctaagataagatgatgtacttgctgatatttttattaaatctttttagcctaactacattttttttttaaaaaaaattcaaacagCTAGGGTATTTGCTTTTCTGTCTGGTGCTCCTGATTATGGAGATGGTCAACTAGACACTAGGAGATATGGTGAACAATATGCTAGCAAAGGGGAAGACCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA