Sequence
atgc intronic sequence ATGC exonic sequence...gaagttaccgttttcgattttgtttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagTGATATGTCTGTTTCACAGGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G314679_T06 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g21250.1 (Oryza sativa), 3'ss of exon 2
gaagttaccgttttcgattttgtttccgataaaaaaatatgaaaacg-gtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagTGATATGTCTGTTTCACAGGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGAT-------------------
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--------------tgcttttgttgatgaacatgaaatgcagcattaagtaactttttctgtcctttgcacaagctcatg----taatgattcatgattgtc--cattttcgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAACGTGTTGCCGTGAAATACTTCTCGGATGATTGGTCTAGTAATGCGTCAA
upper sequence: GRMZM2G314679_T06 (Zea mays), 3'ss of exon 2
lower sequence: AT3G09800.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------gaagttaccgttttcgattttgtttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgtttt------aatccctattcagTGAT------ATGTCTGTTTCACAGGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGAT-------------------
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gtaagtacatatgcattatatgattgtatttcgtattctgttagaatgtgtgtatgttgccgcaatcatacagctttgtaggagttttactctttttttggactggaacttaattactgactttccaatgtacattgaatagGATTCTTGTCCTTTGGTAAAGAAGATTCTTCTTCTAGACTCTGAAGGAAAGCGTGTGGCTGTCAAGTATTACTCGGATGACTGGCCAACTAATGCCGCCA
upper sequence: GRMZM2G314679_T06 (Zea mays), 3'ss of exon 2
lower sequence: AT4G08520.1 (Arabidopsis thaliana), 3'ss of exon 2
gaagttaccgttttcgattttgtttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagTGATATGTCTGTTTCACAGGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGAT-------------------
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---------------gaagttcaaacttacatgatc-cattttaaggattctcgcttctgcttgtgctt-ctctctcttagtacttacatgctgactatctggtcta--caatgaatagGATTCTTGTCCTTTGGTAAAGAACATTCTTCTTCTAGACTCTGAAGGAAAGCGTGTGGCTGTCAAGTATTACTCCGATGATTGGGCAACTAATGCTTCCA
upper sequence: GRMZM2G314679_T06 (Zea mays), 3'ss of exon 2
lower sequence: AT1G60970.1 (Arabidopsis thaliana), 3'ss of exon 1
gaagttaccgttttcgattttgtttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagTGATATGTCTGTTTCACAGGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGAT-------------------
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----ttactgttcactgattcatgttctgttacatcttttggt--tggtgat--tttcaatatctcttaatcttt-------attctattctgtgtttt-cattacttacattt---agGAATTGCCCCCAAAAGTGAAAAACATCTTGCTTTTGGATTCTGAAGGAAAGCGTGTAGCGGTTAAGTATTACTCAGATGACTGGCCAACAAATTCAGCTC
upper sequence: GRMZM2G314679_T06 (Zea mays), 3'ss of exon 2
lower sequence: Vv09s0002g01710.t01 (Vitis vinifera), 3'ss of exon 1
gaagttaccgttttcgattttgtttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagTGATATGTCTGTTTCACAGGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGAT----------------------
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--------ttctttcaatcttttttattttgtttggacatgcattcatca----------tgttaattgttttcttctaatcaattcagattttgttttgttttgt-tttcttttatagG---CTTGCCCCTCTATAAAAAACATTCTTCTTCTGGATTCTGAAGGGAAGCGTGTGGCAGTCAAATATTACTCCGATGATTGGCCAACAAATGCTGCAAAAT
upper sequence: GRMZM2G314679_T06 (Zea mays), 3'ss of exon 2
lower sequence: Vv10s0003g02760.t01 (Vitis vinifera), 3'ss of exon 2
gaagttaccgttttcgattttgt--ttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagTGATATGTCTGTTTCACAGGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGAT-------------------
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-----aaacaaattcaaatttatcattcctatgtagtagt-tgagcaca--------tttagttttcatgaact-----cgcctagtctgatatttatgtaat--tttttttttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAACGTGTAGCTGTCAAGTACTATTGTGACGACTGGCCAACAAATAATGCTAMapped 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|91873753|gb|EB403710.1|EB403710EST: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG TGATATGTCTGTTTCACAGGAATCTTGCCCTTCTGTGAAGAACATTTTACT
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... ccctattcagTGATATGTCTGTTTCACAGGAATCTTGCCCTTCTGTGAAGAACATTTTACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagTGATATGTCTGTTTCACAGGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGAT
ttttaat putative branch site (score: 3)
tccctattc CT-rich tract
ttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaagttaccgttttcgattttgtttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagTGATATGTCTGTTTCACAGGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - -ttttgtt
- - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - atgaaaac