Sequence
atgc intronic sequence ATGC exonic sequencegtatgcttcatatgttcatatctcatgatgtttcaccccccaacccacccctcccccctttttaatttttgttgctcttactctaaaggaaaatttgcagCCCACTGTAGGCCCTGATGGGAAGATAAAGGAGCCTGAGAGCAATGTACTTTTAGCATCAATTGAGAACATGCAATATGCTGTGACGGTGGATGTTCTGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 6
gtatgcttcatatgttcatatctcatgatgtttcaccccccaacccacccctcccccctttttaatttttgttgctcttactctaaaggaaaatttgcagCCCACTGTAGGCCCTGATGGGAAGATAAAGGAGCCTGAGAGCAATGTACTTTTAGCATCAATTGAGAACATGCAATATGCTGTGACGGTGGATGTTCTGC
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--------------------------------gtatgctttaacatttcatactattcgttgtgttctttctctccttccttacagtggaggttatgcagCCCACTTTAGGCCCTGATGGGAAGATAAAGGAGCCTGAGAGCAATGTGCTTTTGGCTTCAATAGAGAACATGCAGTATGCTGTGACGGTGGATGTTCTAC
upper sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 7
gtatgcttcatatgttcatatctcatgatgtttcaccccccaacccacccctcccccctttttaatttttgttgctcttactctaaaggaaaatttgcagCCCACTGTAGGCCCTGATGGGAAGATAAAGGAGCCTGAGAGCAATGTACTTTTAGCATCAATTGAGAACATGCAATATGCTGTGACGGTGGATGTTCTGC
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----------------------gtattttgtttcatgctttaataca---ttctccttttactactttttagtatgtgctaacaatcatataatcttcagACTGCTGTAGGCCCTGATGGGAAGAGGAAAGAACCTGAGAGCAATGTGCTTTTGGCTTCCATTGAAAATATGCAGTATGCTGTTACTGTTGATGTCCTCC
upper sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA18G49580.1 (Glycine max), 3'ss of exon 6
gtatgcttcatatgttcatatctcatgatgtttcaccccccaacccacccctcccccctttttaatttttgttgctcttactctaaaggaaaatttgcagCCCACTGTAGGCCCTGATGGGAAGATAAAGGAGCCTGAGAGCAATGTACTTTTAGCATCAATTGAGAACATGCAATATGCTGTGACGGTGGATGTTCTGC-
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------------------tattttat--tgttttatgctttaataca---ttctccttttattattttttagtatgtgctaacaagcatataatattcagaCTGCTGTAGGCCCTGATGGGAAGAGGAAAGAACCTGACAGCAATGTGCTTTTGGCTTCCATTGAAAATATGCAGTATGCTGTTACTGTTGATGTCCTCCA
upper sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv14s0108g01030.t01 (Vitis vinifera), 3'ss of exon 6
gtatgcttcatatgttcatatctcatgatgtttcaccccccaacccacccctcccccctttttaatttttgttgctcttactctaaaggaaaatt-tgcagCCCACTGTAGGCCCTGATGGGAAGATAAAGGAGCCTGAGAGCAATGTACTTTTAGCATCAATTGAGAACATGCAATATGCTGTGACGGTGGATGTTCTGC
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-----------------------------------gtaaattttttacagttgaatatttattgaaatttttaccatgtactaacaggttgttctatccagCCTGCTTTAGGTCCTGATGGCAAGAAAAAAGAACCTGAGAGTAATGTTCTTCTTGCTTCAATTGAGAATATGCAATATGCTGTTACAGTAGATGTTCTTCMapped 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|101382157|gb|EB813134.1|EB813134EST: CCAATCCTTACCTTCCTGTGAACCAA-CAGCAATTGAAGGGATTGTGCAG CCCACTGTAGGCCCTGATGGGAAAATAAAGGAGCCTGAAAGCAATGTACTT
genomic: CCAATCCTTACCTTCCTGTGAACCAAACAGCAATTGAGGGGATTGTGCAGgtatgcttca ... aaatttgcagCCCACTGTAGGCCCTGATGGGAAGATAAAGGAGCCTGAGAGCAATGTACTT
EST:
gi|6626417|gb|AW257949.1|AW257949EST: CCAATCCTTACCTTCCTGTGAACCAAACAGCAATTGAGGGGATTGTGCAG CCTACTGTAGGCCCTGATGGGAAGATAAAGGAGCCTGAGAGCAATGTACTT
genomic: CCAATCCTTACCTTCCTGTGAACCAAACAGCAATTGAGGGGATTGTGCAGgtatgcttca ... aaatttgcagCCCACTGTAGGCCCTGATGGGAAGATAAAGGAGCCTGAGAGCAATGTACTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacccctcccccctttttaatttttgttgctcttactctaaaggaaaatttgcagCCCACTGTAGGCCCTGATGGGAAGATAAAGGAGCCTGAGAGCAATGTACTTTTAGCATCAATTGAGAACATGCAATATGCTGTGACGGTGGATGTTCTGC
ctctaaa putative branch site (score: 3)
tttttaatttttgtt 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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gtatgcttcatatgttcatatctcatgatgtttcaccccccaacccacccctcccccctttttaatttttgttgctcttactctaaaggaaaatttgcagCCCACTGTAGGCCCTGATGGGAAGATAAAGGAGCCTGAGAGCAATGTACTTTTAGCATCAATTGAGAACATGCAATATGCTGTGACGGTGGATGTTCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA