Sequence
atgc intronic sequence ATGC exonic sequence...ggaaaatgagctactcaatccccgggaatcccagaggggatttaagtttccaaactagccctaaataaacaagtaatgactctggttttctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 13
ggaaaatgagctac----tcaatccccgggaatcccagaggggatttaagtttccaaactagccctaaataaacaagtaatgactctggttttctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
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gagaagccattcacagcgcaaacacttgggtgtcttgtaatg---tttactgttggtatttattatgagcaagaagccaagaactg-acttgaatgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGGTTCTATGTCACTGCCTTGGC
upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 13
-----------ggaaaatgagctactcaatccccgggaatcccagaggggatt---taagtttccaaactagccctaaataaacaag-taatgactctggtttt--ctgttc--tccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
||| | | || || | | | | || || || || | ||| | | |||| | | ||| ||| || || | ||| || || || ||||| ||||| ||||| |||||| | ||||| || |||||||| ||||||||||||| || || || |||||||||||||||||
gttaatacccctgaagtttttattcttcatgtattgtatttggggtggcaataatatacgtattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAATGGATCAACAAAAAGTGGAGAGAAGGATTTTATGTCACTGCTATGGC
upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 13
ggaaaatgagctactcaatccccgggaatcccagaggggatttaagtttccaaactagccctaaataaacaagtaatgactctggttttctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
| || | || | || | | || | ||||| || | | | | ||||| || | | || ||||||| ||||| ||| ||||| || |||||||| |||||| |||||||||| || ||||| ||||||||||||| ||||||||| || || ||||| |||||
---------gttagttcctcttaaagtatat-atcgcctatgtcagtttggcaatt--ttcaattttgttttccgctgactatgatct--tggactccagGCACACAGTATTTGCAGCAATCATACAAAGTTAGTGATTCATTTCCTTTTAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTGCAATGGC
upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
------------ggaaaatgagctactcaatccccgggaatcccagaggg----gatttaagtttccaaactagccctaaataaacaag-taatgactctggtttt--ctgttc--tccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
| | | | ||| | | || | || || || | | ||| | | |||| | | ||| ||| || || | ||| || || || ||||| ||||| ||||| |||||| | ||||| || || ||||| |||||||| |||| || || || |||||||||||||||||
gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 13
----------------------------------------------ggaaaatgagctactcaatccccgggaatcccagagg--ggatttaagtttccaaactagccctaaataaacaag-taatgactctggtttt--ctgttc--tccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
| || | || | | ||| || | ||| | | ||| | | ||||| | | ||| ||| || || | ||| || || || ||||| ||||| ||||| |||||| ||||||| || || ||||| |||||||| |||| || || || |||||||||||||||||
gttaatcccctgaagtatttattcttcatgtattgtgtctttgggatggcgataattggcttgagtttagatgatcacatgttttgcttttgcatattttgactggttatgtttaaactgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTGCAGCAATCCTATAAAGTCAGTGATTCATTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 13
ggaaaatgagctactcaatccccgggaatcccagaggggatttaagtttccaaactagccctaaataaacaagtaatgactctggttttctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
| || | | | | | || || | | ||| || | | | | ||||| || | | || ||||||| ||||| ||| ||||| || || ||||| ||||| ||||||||||||| ||||| ||||||||||||| ||||||||| || || ||| | |||||
---------gttagt--acctctaaagtatatattggcaatgtcaatttggcaaat--ttcaattttgttttccgctgactatgatct--tggactccagGCACACAGTATTTGCAGCAATCATATAAAGTTAGTGACTCATTTCCTTTCAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTTCAATGGC
upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 13
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
ggaaaatgagctactcaatccccgggaatcccagaggggatttaagtttccaaactagccctaaataaacaagtaatgactctggttttctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
|| | | ||| |||| | || | | ||||| || | || | | | | | | ||| || ||| || || ||| || || ||||||||||| |||||| | ||||| ||||| |||||||| |||||||||| ||| || || ||||| || | |||||
---gtattcttgttttactccttttgaatgc-aggtgtaacagttatttccgttttatctctgtttc--------acagttttcatcatttgtattc-agGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 13
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 13
-ggaaaatgagctactcaatccccgggaatcccagaggggatttaagtttccaaactagccctaaataaacaagtaatgactctggttttctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
| ||| || | || || | | ||| || || | | | | | | ||| || | ||| | ||| || |||||| ||||||||||| ||||| ||||| ||||||| || || |||||||| ||||| |||| ||||| |||||||| |||||||||||
gtcagtgtgacttatttaaaaccaatcattttttgagacaatgacttcttttatgattgttatctgtct-cttttaacctctgttaatttactgaatatagGCACGCAATATTTACAGCAGTCCTATAAAGTCAGTGAGTCATTTCCATTTAAGTGGATAAATAAAAAATGGAGAGAGGGTTTCTATGTTACTGCTATGGC
upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 13
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 13
ggaaaatgagctactcaatccccgggaatcccagaggggatttaagtttccaaactagccctaaataaacaagtaatgactctggttttctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
| | || | | |||||| | | ||| | | | | | ||||| || || ||||||| |||||||| || ||||| |||||||| |||||| ||||||| ||||| |||||||| ||||| |||| |||||| ||||||||||| |||||||
-------------gttagtctaacatatttggctgatggatttctatgacaaaatttatctatattttgc-----ttgacttcatttcattga-ctccagGTACACAATACTTGCAACAGTCTTACAAAGTTAGTGATTCATTTCCCTTCAAGTGGATAAATAAAAAATGGAGGGAGGGTTTCTATGTCACCTCTATGGC
upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 13
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 11
ggaaaatgagctactcaatccccgggaatcccagaggggatttaagtttccaa-actagccctaaataaacaagtaatgactctggttttctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
| ||| | | | | ||| | |||| | |||| | | |||| |||| ||| | || || || |||||||| || ||| ||||||| ||||| ||||| ||||||||||||| ||| || || || || ||| | |||||
-------------------------------------gtattgtcgctgttattgatggccactggc--attgtcgctgacgcgtgtttcc---cccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC
upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 13
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 11
ggaaaatgagctactcaatccccgggaatcccagaggggatttaagtttccaa-actagccctaaataaacaagtaatgactctggttttctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
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-------------------------------------gtattgtcgctgttattgatggccactggc--attgttgctgacgcgtgattcc---cccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGCMapped 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|67025278|gb|CO454027.1|CO454027EST: TGCACTGGCTGGTGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAG GAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCA
genomic: TGCACTGGCTGGTGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAGgtaattacat ... tgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCA
EST:
gi|9956162|gb|BE643596.1|BE643596EST: GCTCTTTGGTGATTATGTCAAGAG GAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCA
genomic: GCTCTTTGGTGATTATGTCAAGAGgtaattacat ... tgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttccaaactagccctaaataaacaagtaatgactctggttttctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
ccctaaa putative branch site (score: 3)
ttttctgttctcc putative PPT
taaataaacaagtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggaaaatgagctactcaatccccgggaatcccagaggggatttaagtttccaaactagccctaaataaacaagtaatgactctggttttctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG