Sequence
atgc intronic sequence ATGC exonic sequencegtgcattgctttttcttttttcttttctttttccttacagacaggtgcattgatttgcatgttactcaaattgtctcctgttatatgatttattacctgttcaccttttgtttgtaattgatttctttcagTGGGCAAATGTTACGAGATGGGAGATGCGGACAAAACCATTTGTGAGGACTCTTGAATTTCTCTGGCAAGAGGGCCACACTGCTCATGCCACCCCTGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0050g00960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os07g07060.1 (Oryza sativa), 3'ss of exon 2
gtgcattgctttttcttttttcttttctttttccttacagacaggtgcattgatttgcatgtt--actcaaattgtctcctgttatatgatttattacctgttcaccttttgtttgtaattgatttctttcagTGGGCAAATGTTACGAGATGGGAGATGCGGACAAAACCATTTGTGAGGACTCTTGAATTTCTCTGGCAAGAGGGCCACACTGCTCATGCCACCCCTGAAG
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--------------------------------------------gtaactctatctgcatatttgaatcaacatgagtcca---atatcattta----ctgtactgatttttcttgttacc--------ctagTGGGCTAATGTCACAAGATGGGAAATGAGGACTAAGCCATTCATCAGAACTCTTGAATTTCTATGGCAAGAAGGTCATACAGCTCATGCCACCCTTGAAG
upper sequence: Vv16s0050g00960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G107089_T02 (Zea mays), 3'ss of exon 3
gtgcattgctttttcttttttcttttctttttccttacagacaggtgcattgatttgcatgttactcaaattgtctcctgttatatgatttattacctgttcaccttttgtttgtaattgatttctttc-agTGGGCAAATGTTACGAGATGGGAGATGCGGACAAAACCATTTGTGAGGACTCTTGAATTTCTCTGGCAAGAGGGCCACACTGCTCATGCCACCCCTGAAG
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--------------------------------------------gtaactttgttggcaattt---taggctagctgtagagttgtagtccactat-tattcacgatat-taaatagttcttatattcctagTGGGCTAACGTGACAAGATGGGAAATGCGGACTAAACCATTCATCCGAACTCTTGAATTTTTATGGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGG
upper sequence: Vv16s0050g00960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G24670.1 (Glycine max), 3'ss of exon 4
gtgcattgctttttcttttttcttttctttttccttacagacaggtgcattgatttgcatgttactcaaattgtctcctgttatatgatt-tattacctgttcaccttttgtttgtaattgatttctttcagTGGGCAAATGTTACGAGATGGGAGATGCGGACAAAACCATTTGTGAGGACTCTTGAATTTCTCTGGCAAGAGGGCCACACTGCTCATGCCACCCCTGAAG
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---------------------------------------------------gtaatgc-tgttg-tgagtttatttctgagcaagaacttgcattgttgaatgacgggacaattttgccaacttgctttcagTGGGCAAACGTGACAAGATGGGAGATGCGCACCAAACCATTTGTGAGAACTCTTGAATTTCTTTGGCAAGAAGGACATACTGCTCATGCAACTCCAGAGG
upper sequence: Vv16s0050g00960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G29890.1 (Glycine max), 3'ss of exon 4
gtgcattgctttttcttttttcttttctttttccttacagacaggtgcattgatttgcatgttactcaaattgtctcctgttatatgatttattacctgttcaccttttgtttgtaattgatttctttcagTGGGCAAATGTTACGAGATGGGAGATGCGGACAAAACCATTTGTGAGGACTCTTGAATTTCTCTGGCAAGAGGGCCACACTGCTCATGCCACCCCTGAAG
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-------------------------------------------------gtaatgctgttgagagtttatttgtgagcaagaacttgctttgttgaatgatgggacaatttttctaact---tgctttcagTGGGCAAACGTGACAAGATGGGAGATGCGCACTAAACCATTTGTGAGAACTCTTGAATTTCTTTGGCAAGAAGGACATACTGCTCATGCAACTCCAGAAG
upper sequence: Vv16s0050g00960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G52520.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgcattgctttttcttttttcttttctttttccttacagacaggtgcattgatttgcatg--ttactcaaattgtctcctgttatatgatttattacctgttcaccttttgtttgtaattgatttctttcagTGGGCAAATGTTACGAGATGGGAGATGCGGACAAAACCATTTGTGAGGACTCTTGAATTTCTCTGGCAAGAGGGCCACACTGCTCATGCCACCCCTGAAG
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------------------------------gtctggacagacattca-attgtttatcattctttgtatgaaaaatctggtatt-tatgactgtt--cctggttatgtttttcttctttctg---cgatttagTGGGCCAATGTCACTAGATGGGAAATGCGGACGAAACCATTTATTAGGACTCTTGAATTTCTATGGCAAGAGGGTCATACTGCTCATGCCACTCCTGAGGMapped 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|110711045|gb|EE087798.1|EE087798EST: TCACTCAGTGGATTCATAGCTACCGTGATCTTCCTCTCATGATTAATCAG TGGGCAAATGTTACGAGATGGGAGATGCGGACAAAACCATTTGTGAGGACT
genomic: TCACTCAGTGGATTCATAGCTACCGTGATCTTCCTCTCATGATTAATCAGgtgcattgct ... tttctttcagTGGGCAAATGTTACGAGATGGGAGATGCGGACAAAACCATTTGTGAGGACT
EST:
gi|27586757|gb|CB009452.1|CB009452EST: GTGGATTCATAGCTACCGTGATCTTCCTCTCATGATTAATCAG TGGGCAAATGTTACGAGATGGGAGATGCGGACAAAACCATTTGTGAGGACT
genomic: GTGGATTCATAGCTACCGTGATCTTCCTCTCATGATTAATCAGgtgcattgct ... tttctttcagTGGGCAAATGTTACGAGATGGGAGATGCGGACAAAACCATTTGTGAGGACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgttatatgatttattacctgttcaccttttgtttgtaattgatttctttcagTGGGCAAATGTTACGAGATGGGAGATGCGGACAAAACCATTTGTGAGGACTCTTGAATTTCTCTGGCAAGAGGGCCACACTGCTCATGCCACCCCTGAAG
aattgat putative branch site (score: 4)
tttctttc CT-rich tract
tatatgatttatta 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
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gtgcattgctttttcttttttcttttctttttccttacagacaggtgcattgatttgcatgttactcaaattgtctcctgttatatgatttattacctgttcaccttttgtttgtaattgatttctttcagTGGGCAAATGTTACGAGATGGGAGATGCGGACAAAACCATTTGTGAGGACTCTTGAATTTCTCTGGCAAGAGGGCCACACTGCTCATGCCACCCCTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG