Sequence
atgc intronic sequence ATGC exonic sequence...agtggtattgctaattctgtttcccccttggccatggtactatagcattaatattgatggacaaatacatagtcatctgactagcaaaatctttttttagATATAACAACTGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 8
agtggtattgctaattctgtttcccccttggccatggtactatagcattaatattgatggacaaatacatagtcatctgactagcaaaatcttttttt---agATATAACAACTGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA
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--atctatt-ttacttcagcttttcaatgatctaatcatgcattgcaataccattttagtttattggagttatcttataattgaaaaaactgttttattgcagACATCACAACGGCAGCAGTTGCTAAACAAGCTTTGGAAGGGCACTGCATATATGATGGAGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA
upper sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 9
-----agtggtattgctaattct---gtttcccccttggccatggtactatagcattaatattgatggacaaatacatagtcatctgactagcaaaatctttttttagATATAACAACTGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA
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aatggaaccaggtagcagatttactagcccccctcctgttcctggttcttgatgaagcattttttt----ttgttcttgatcat--gagta--aacatttttttgcagATATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGA
upper sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA11G21330.1 (Glycine max), 3'ss of exon 8
-agtggtat-tgctaattctgtttcccccttggccatggtactatagcattaatattgatggacaaatacatagtcatctg--actagcaaaatct-ttttttagATATAACAACTGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA
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gtgaaatatattctcattttgtttttctag-ggtcat----cctttgcttgacatttggttgtgtattcagcatgcatctgtaactatttttattcgtctttcagATATCGCCACAGCAACAGCTGCCAAAAAAGCTCTAATGGGGCATTGCATATATGATGGTGGCTGTTGTAAGCTTCGTCTATCATACTCTCATCATACTGA
upper sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA18G49580.1 (Glycine max), 3'ss of exon 8
-------agtggtattgctaattctgtttcccccttggccatggtactatagcattaatattgatggacaaatacatagtcatctgactagcaaaatctttttttagATATAACAACTGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA-
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ggaatggaactgggtagcagatttactagccctcctgtgcgtgtttcttgatga--aacatt--tgtttttgttcttgatcatgtg--ta--aacatttttttgcagaTATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGAT
upper sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT3G01150.2 (Arabidopsis thaliana), 3'ss of exon 6
----------------agtggtattgctaattctgtttcccccttggccatggtactatagcatt--aatattgatggacaaatacatagtcatct---gactagcaaaatctttttt-------tagATATAACAACTGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA
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gtacatccgactgctgatctgcactaatgtttgattgtgacccgattcaaccgttttataaattctgaacatttatttgttactgtacaatcatcttcagtttcgtgctttctatttcgtctctgtagATATACCAACAGCAGCAATGGCCAAAGAAGCACTGGAAGGACACTGCATTTATGACGGTGGCTACTGTAAGCTTCGACTATCATACTCTCGTCATACTGA
upper sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv14s0108g01030.t01 (Vitis vinifera), 3'ss of exon 8
agtggtattgctaattctgtttcccccttggccatggt--actatagcattaatattga-----tggacaaatacatagtcatctgactagcaaaatctttttttagATATAACAACTGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA
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----tcaattttatttcta--ccaccatagggaatggttggcaattttatttatatctcatccctccactgctgggcagacaaatgatctgttgt-tttctttccagATGTCACAACTGCAGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGA
upper sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S326_1V6.1 (Physcomitrella patens), 3'ss of exon 8
agtggtattgctaattctgtttcccccttggccatggtactatagcattaatattgatggacaaatacatagtcatctgactagcaaaatcttttttt---agATATAACAACTGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA
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---agtgtcaagagctctgagattgtgctggatggtttattagcggccttttaatatggttctagctagcatccaacgagtttttgctttttttcttctacagATATTCCTACTGCAGTTGGAGCAAAAGAAGCACTCGAAGGTCACTGCATTTACGATGGCGGTTTCTGCAAGCTTCATCTATCATACTCTCGGCATACTGAMapped 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|6626417|gb|AW257949.1|AW257949EST: TGCCATGTTTGAGAAGAATGGTGGAATGCAGGCTCTAATTCAATATCCAG ATATAACAACTGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATAT
genomic: TGCCATGTTTGAGAAGAATGGTGGAATGCAGGCTCTAATTCAATATCCAGgtatatgctc ... ctttttttagATATAACAACTGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattaatattgatggacaaatacatagtcatctgactagcaaaatctttttttagATATAACAACTGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA
atctgac putative branch site (score: 3)
tcttttttt putative PPT
aaaatcttttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtggtattgctaattctgtttcccccttggccatggtactatagcattaatattgatggacaaatacatagtcatctgactagcaaaatctttttttagATATAACAACTGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG