Sequence
atgc intronic sequence ATGC exonic sequencegtatgctttgatgctcagtaccttaattcattttttttttttcctgaaggaatatttttctttgtagaaacttaccattttatatctagaatatctcatattatcatcctcttgctcttgtttccacattgtaacttcagGTTGTACACCTCTCCATTGGGCTGCTATTAGGGGCAACTTAGAGGCATGCACAGTGTTAGTGCAGGCTGGGAAGAAGGAGGACCTAATGATGACCGACAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os06g43680.1 (Oryza sativa), 3'ss of exon 4
gtatgctttga---tgctcagtacc-ttaattcattttttttttttcctgaaggaatatttttctttg---tagaaacttaccattttatatctagaatatctcatattatcatcctcttgctcttgtttccacattgtaacttcagGTTGTACACCTCTCCATTGGGCTGCTATTAGGGGCAACTTAGAGGCATGCACAGTGTTAGTGCAGGCTGGGAAGAAGGAGGACCTAATGATGACCGACAA
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gcatgtgctaaatttatctatttccattattacctgtactgctgtgcacataacagtgtaaaccaatggcttagccatatctccaattatatc-agtacacttcagagcatgagatttacttctttactacaatgctgc--ccctagGTTGTACCCCTTTACATTGGGCTGCTATTAGGGGGAACCTGGAGGCATGCACTGTGCTAGTTCAGGCTGGCAAAAAGGATGACTTGATGGTGAAGGATAA
upper sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G024437_T01 (Zea mays), 3'ss of exon 4
gtatgctttgatgctcagtaccttaattcattttttttttttcctgaaggaatatttttctttgtagaaacttaccattttatatctagaatatctcatattatcatcctcttgctcttgtttccacattgtaacttcagGTTGTACACCTCTCCATTGGGCTGCTATTAGGGGCAACTTAGAGGCATGCACAGTGTTAGTGCAGGCTGGGAAGAAGGAGGACCTAATGATGACCGACAA
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-------------------------gcatgtgtaaatttattcc---atgcctatatta-tttataataatt---cctttggtaattatatcagcttatttgg--atgatatttcttttaactgcgcatgctactcttagGTTGTACTCCTTTACACTGGGCTGCTATTCGGGGGAACCTTGAGGCATGCACTGTGCTAGTTCAGGTTGGCAAAAAGGATGATTTGATGGTGAAAGACAA
upper sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 4
gtatgctttgatgctcagtaccttaattcattttttttttttcctgaaggaatatttttctttgtagaaacttaccattttatatctagaatatctcatattatcatcctcttgctcttgtttccacattgtaacttcagGTTGTACACCTCTCCATTGGGCTGCTATTAGGGGCAACTTAGAGGCATGCACAGTGTTAGTGCAGGCTGGGAAGAAGGAGGACCTAATGATGACCGACAA
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gtatgttctaatgctctat-cctgaactccatttattcccctc--------aaattattcat-gcactaaatgatgaattgatctttgat---tttgaaagcattat--tctagtttttattttcc--ttattcgttcagGTTGCACTCCTCTTCATTGGGCTGCTATTAGGGGCAACTTGGAGGCCTGTACCGTGCTAGTACAGGCTGGCAAGAAGGAAGATCTTATGCTGGCTGATAA
upper sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 5
gtatgctttgatgctcagtaccttaattcattttttttttttcctgaaggaatatttttctttgtagaaacttaccattttatatctagaatatctcatattatcatcctcttgctcttgtttccacattgtaacttcagGTTGTACACCTCTCCATTGGGCTGCTATTAGGGGCAACTTAGAGGCATGCACAGTGTTAGTGCAGGCTGGGAAGAAGGAGGACCTAATGATGACCGACAA
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gtatgttctaatgctctatcctgaactccatgtattctcctt---------aaattattcat-gcactaaatgatgaaccgatctttgat---tttcaaagcattat--tctagttttatttttcttaattta--ttcagGTTGCACTCCTCTTCATTGGGCTGCTATTAGGGGCAACTTGGAGGCCAGTACCGTGTTAGTACAGGCTGGCAAGAAGGAAGATCTTATGGTGACTGATAAMapped 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|161721152|gb|FC071027.1|FC071027EST: ACGTCTTCTTTTATTTCTGGACGCATATAGGGGACGCCAGGATAAAGAGG GTTGTACGCCTCTCCATTGGGCTGCTATTAGGGGCAACTTAGAGGCATGCA
genomic: ACGTCTTCTTTTATTTCTGGACGCATATAGGGGACGCCAGGATAAAGAGGgtatgctttg ... gtaacttcagGTTGTACACCTCTCCATTGGGCTGCTATTAGGGGCAACTTAGAGGCATGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctagaatatctcatattatcatcctcttgctcttgtttccacattgtaacttcagGTTGTACACCTCTCCATTGGGCTGCTATTAGGGGCAACTTAGAGGCATGCACAGTGTTAGTGCAGGCTGGGAAGAAGGAGGACCTAATGATGACCGACAA
ttgtaac putative branch site (score: 2)
atatctcatattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctttgatgctcagtaccttaattcattttttttttttcctgaaggaatatttttctttgtagaaacttaccattttatatctagaatatctcatattatcatcctcttgctcttgtttccacattgtaacttcagGTTGTACACCTCTCCATTGGGCTGCTATTAGGGGCAACTTAGAGGCATGCACAGTGTTAGTGCAGGCTGGGAAGAAGGAGGACCTAATGATGACCGACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA