Sequence
atgc intronic sequence ATGC exonic sequenceGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaacatttggtgttcttttaagtaggatagatgggcgtatccataatatcctcaacctcaaatggtaaaatgaaccatacacttggaaaaaac...
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 5'ss of exon 6
GAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaacatttggt-------gttcttttaagtaggatagatg-ggcgtatcca-taatatcctcaacctcaaatggtaaaatgaaccatacacttggaaaaaac
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AAGTCCAGAAGTTGTGAAAAGGTGGAGCAATGAAGTTCAGGAGGCTGTACAGTCGAGAGCTGCTCTTGTTCAATTTCATGCCCTTGCTCTTCTTCACCAGgtgagatttatgtttggtttttactactccctccatcccaaaatataaggcataaccactcataacacaaagaccaagaaa-acatttaaccaccttcttg--------
upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA11G12610.2 (Glycine max), 5'ss of exon 6
GAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaacatttggtgttcttttaagtagga-tagatgggcgtatccataatatcctcaacctcaaatggtaaaatgaaccatacacttggaaaaaac-
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AAATCCTGAGATTGTAAAAAGGTGGAGCAATGAGGTTCAGGAAGCGGTTCAATCAAGGGCAGCTCTTGTGCAATTTCATGCCCTGGCATTGCTGCACCAGgtatgttgcgttgtgtgaatggtttgatgttgtagtttcttggcaagcttatcaaatca-caatc-caaatcatgaatcgattggttaatttttgaatcatg
upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA12G04820.1 (Glycine max), 5'ss of exon 6
GAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaacatttggtgttcttttaagtagga--tagatgggcgtatc-cataatatcctcaacctcaaatggtaaaatgaaccatacacttggaaaaaac
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AAATCCCGAGATTGTAAAAAGATGGAGTAATGAGGTTCAGGAAGCTGTTCAATCAAGGGCAGCTCTTGTGCAATTTCATGCCCTGGCTTTGCTGCATCAGgtatgttgcgttgcatgaatggtttgatgttgtagtttcttgacaatattaccaaatgatccaaatcatgaatcgtttggctaatttttgaatcatgaat---
upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA04G01470.1 (Glycine max), 5'ss of exon 6
GAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaacatttggtgttcttttaagtaggatagatgggcgtatccataatatcctcaacctcaaatggtaaaat-gaaccatacacttggaaaaaac-
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AAATCCTGAAATTGTAAAAAGATGGAGCAATGAGGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTGCATCAGgtatgcttccaaaattatttggttctgtacagggtttttgg-tgtattaa-agcacctcaaaactttgtcatcattctagggtcatttagtgtatcaaagtt
upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA06G01520.1 (Glycine max), 5'ss of exon 6
GAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaacatttggtgttcttttaagtaggatagatgggcgtatccataatatcctcaacctcaaatggtaaaat-gaaccatacacttggaaaaaac-
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GAATCCTGAAATTGTAAAAAGATGGAGCAATGAAGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTACATCAGgtatgcttccaaaattatttggctctgtacagggtttttgg-tgtattaa-agcacctcaaaacttggtcttcattctagggtcatttagagtatcaaagtg
upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 5'ss of exon 5
GAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaacatttggtgttcttttaagtaggatagatgggcgtatccataatatcctcaacctcaaatggtaaaatgaaccatacacttggaaaaaac---
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AAACCCAGAAATTGTTAAAAGATGGAGCAATGAAGTTCAAGAAGGTATTCAATCCAGATCAGCCCTTGTTCAGTTCCATGCCCTAGCTTTGCTCCATCAGgttagtttgttgcattattatcaccgaagtcg-attggtctatgtttctactctttgtttaa--ttaaacagccactgagaagaagtatctcggaaaatgaga
upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 5'ss of exon 6
GAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaacatttggtgttcttttaagtaggatagatgggcgtatccataatatcctcaacctcaaatggtaaaatgaaccatacacttggaaaaaac---
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AAACCCAGAGATAGTGAGAAGGTGGAGTAATGAAGTACAGGAAGCTGTTCAATCAAGGGCAGCACTTGTGCAATTTCATGCCCTAGCTCTCCTGCATCAGgtatgttggattttt--tggttccatgtttaagtttaaattcagaatacagagtagcttgttagaaagatagttcc-tgaacttcatagaggtaaaattttgc
upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S41_154V6.1 (Physcomitrella patens), 5'ss of exon 6
GAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaacatttggtgttcttttaagtaggatagatgggcgtatccataatatcctcaacctcaaatggtaaaatgaacc-atacacttggaaaaaac-------
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CAATCCCGAAATTGTGAAGCGATGGAGTAATGAAGTTCAAGAGGCTGTTCAGTCCAAGGCACCACTTGTTCAGTTCCATGGTTTGGCATTGCTTCATCAGgtcagttttctttcatacactgttttttcccctcttgat--------ttaccatttttacgaattgtcgttgtgtaggacacctgttcactcaggattgtccacggtgMapped 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|18655281|gb|BM500086.1|BM500086EST: AGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAA ATTAGACAAAATGATCG
genomic: AGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaa ... gatgtttcagATTAGACAAAATGATCG
EST:
gi|148956209|gb|EC901999.2|EC901999EST: AGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAA ATTAGAACAAA-TGATCGGTTGGCTGTCAGCAAGCTTGTCACTAGCTTGAC
genomic: AGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaa ... gatgtttcagATTAGA-CAAAATGATCGGTTGGCTGTCAGCAAGCTTGTCACTAGCTTGAC
EST:
gi|22490147|gb|BU050070.1|BU050070EST: AGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAA ATTAGACAAAATGATCGGTTGGCTGTCAGCAAGCTTGTCACTAGCTTGACC
genomic: AGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaa ... gatgtttcagATTAGACAAAATGATCGGTTGGCTGTCAGCAAGCTTGTCACTAGCTTGACC
EST:
gi|148931355|gb|EC874250.2|EC874250EST: AGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAA ATTAGACAAAATGATCGGTTGGCTGTCAGCAAGCTTGTCACTAGCTTGACC
genomic: AGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaa ... gatgtttcagATTAGACAAAATGATCGGTTGGCTGTCAGCAAGCTTGTCACTAGCTTGACC
EST:
gi|87153597|gb|DY398386.1|DY398386EST: AGTCAAGAGCTGCTCTTGTGCAATATCATGCCCTTGCTCTTCTTCACCAA ATTAGACAAAATGATCGGTTGGCTGTCAGCAAGCTTGTCACTAGCTTGACC
genomic: AGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaa ... gatgtttcagATTAGACAAAATGATCGGTTGGCTGTCAGCAAGCTTGTCACTAGCTTGACC
EST:
gi|60396049|gb|DN228919.1|DN228919EST: AGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAA ATTAGACAAAATGATCGGTTGGCTGTCAGCAAGCTTGTCACTAGCTTGACC
genomic: AGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaa ... gatgtttcagATTAGACAAAATGATCGGTTGGCTGTCAGCAAGCTTGTCACTAGCTTGACC
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 4 RNA-Seq libraries.
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
109GAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaa ... gatgtttcagATTAGACAAAATGATCGGTTGGCTGTCAGCAAGCTTGTCACTAGCTTGACCAGGGGTTCAGTTCGCTCTCCGTTGGCCCAGTGCCTACTTATTCGCTACA
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
166GAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaa ... gatgtttcagATTAGACAAAATGATCGGTTGGCTGTCAGCAAGCTTGTCACTAGCTTGACCAGGGGTTCAGTTCGCTCTCCGTTGGCCCAGTGCCTACTTATTCGCTACA
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
55GAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaa ... gatgtttcagATTAGACAAAATGATCGGTTGGCTGTCAGCAAGCTTGTCACTAGCTTGACCAGGGGTTCAGTTCGCTCTCCGTTGGCCCAGTGCCTACTTATTCGCTACA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
150GAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaa ... gatgtttcagATTAGACAAAATGATCGGTTGGCTGTCAGCAAGCTTGTCACTAGCTTGACCAGGGGTTCAGTTCGCTCTCCGTTGGCCCAGTGCCTACTTATTCGCTACA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACCAAgtgagttaaacatttggtgttcttttaagtaggatagatgggcgtatccataatatcctcaacctcaaatggtaaaatgaaccatacacttggaaaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaaaaa