Sequence
atgc intronic sequence ATGC exonic sequence...ccttaatttgatttgcactcagctgacaatcgggagagattattttctcagctaacaattatattgcgccctaacgatctcatcggtgccttcttaccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g63750.1 (Oryza sativa), 3'ss of exon 1
ccttaatttgatttgcactcagctgacaatcgggagagattattttctcagcta-acaattatattgcgccctaacgatctcatcggtgc-cttcttaccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
| || | | || |||| | | | | || || || | | | | | ||||||||||||| ||||| ||| | | ||||| ||||| || ||||||||||| || ||||| |||||||| || |||||||| ||||||||||| ||||| |||||||| ||||||||||||||||||
--atcatataacactcagtcagaagtacttgtaccgggcagatacactgtgccatgtacgttagccggcctctaacgatctcattggtgcacttatgagcagGGATTTAGGAAAGTTGATCCAGATAGGTGGGAGTTTGCAAACGAAGGTTTTCTTAGAGGACAAAAGCATCTACTGAAGACCATCAACAGAAGGAAACCAA
upper sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G44330.1 (Glycine max), 3'ss of exon 1
ccttaatttgatttgcactcagctgacaatcgggagagattattttctcagctaacaattatattgcgccctaac--gatctcatcggtgccttcttaccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
| ||||| || || || | ||| | ||||| || || | ||| | | | | ||| | | | | || | | ||||| |||||||||||||| ||||| ||||||||||||||||||| || ||| | ||||| ||||||| || | || | ||||| || ||||| |
gcataattaacattacatgtagtt--ttatcaagctggattagttgtacaattcacacatttctcttctcttaatctgttattctttttgattgacaagcagGGTTTTAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
upper sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G01190.1 (Glycine max), 3'ss of exon 1
ccttaatttgatttgcactcagctgacaatcgggagagattattttctcagctaacaattatattgcgccctaac--gatctcatcggtgccttcttaccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
| | ||| | || || | || | ||| | ||||| || ||| | ||| | | | | ||| | | || | | ||||| || ||||||||||| ||||| ||||||||||||||||||| || ||| | ||||| ||||||| || | || | ||||| || ||||| |
gcattattagcattacatttagtt--ttatcaagctggattagttgtacagttcacacatttttcttctcttaatttgttactccttttgattgacaaacagGGTTTCAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
upper sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G13400.1 (Glycine max), 3'ss of exon 1
ccttaatttgatt-tgcactcagctgacaatcgggagagattattttctcagctaacaattatattgcgccctaacgatctcatcggtgccttcttac-cagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
||| |||| || |||| | | | | | | | ||| | | | | || | |||| ||| | | | | ||| ||||| ||||| ||||| |||||||| | |||||||||||||||||||| ||| |||| || ||||| || |||| |||||||| | | |||||||
-tttagtttgtttgtgcatgccaaaactataatgttgtgtatgtcaaatcaaacatcgacctt-ttcctttctaatatcatcaacaattcatcattaagcagGGATTTAGGAAGGTAGATCCAGATCGCTGGGAATTTGCAAATGAGGGATTTTTGAGGGGTCAAAAGCACTTGCTTAAGACTATAACTCGGCGGAAACCTG
upper sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G33920.1 (Glycine max), 3'ss of exon 2
ccttaatttgatttgcactcagctgacaatcgggagagattattttctcag-ctaacaattatattgcgccctaacgatctca--tcggtgccttcttaccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
| | | | | | | | | | | || | | | | || || | || | ||||| ||| || | | | ||| |||| || || |||||||||||||| | |||||||||||||||||||||||| |||| || ||||| || |||| | || ||| | ||| | |||||
--tctgtgttttatataacaactcaagctgtgtgccttttcatatgccctgtcttttttttctcttcctttctaacatcgtcaattcattatcattatac-agGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAGGGGTCAAAAGCACTTGCTTAGGAGTATAACAAGACGAAAACCTG
upper sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G01990.1 (Glycine max), 3'ss of exon 1
-ccttaatttgatttgcactcagctgacaatcgggagagattattttctcagctaacaattatattgcgccctaacgatctcatcggtgccttcttac----cagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
|| | | ||| | | || | || ||| || | || | || | | | ||||| | | || | | ||||| || || |||||||||||||| | |||||||||||||||||||||||| ||| || ||||| || |||| | || ||| | || | |||||
ataacaactcaagttgtgtgccttt-----tcagagtgtgttgacctctgtcctgtcttttcttttttccttttctaacgtcatcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAAGGGTCAAAAGCACTTGCTTAGGAGTATTACACGACGAAAACCTG
upper sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT4G17750.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------------------------ccttaatttgatttgcactcagctgacaatcgggagagattattttctcagctaacaattatattgcgccctaacgatctcatcggtgccttcttac---cagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
|| | ||| || || | | || | || || || | | | | | | || |||| | || | | ||||| ||||| || || |||||||| ||||||||||||| ||||| ||||| | ||||| ||||||||||| |||||| || | | | || ||| |
gtaagtataaattctctcgcgccctaatttctccaccattgatttctctaattgtactgtgtatagattatgatttcgttgaataatcttagtgcttgatgtgtttgataagatttatatgattcatgtgccaattttgatgaacagGGTTTTAGGAAAGTGGATCCAGATCGATGGGAATTTGCTAATGAAGGTTTCTTAAGAGGTCAAAAACATCTATTGAAGAAGATAAGCCGGAGAAAATCTG
upper sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT3G02990.1 (Arabidopsis thaliana), 3'ss of exon 1
ccttaatttga--tttgcac-tcagctgacaatcgggagagattattttctcagctaacaattatattgcgccctaacgatctcatcggtgccttcttaccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
|| || | || | | ||| | || | | || || | || | | | | | || | ||| || ||||| |||||||| |||||||||||| | ||||| |||||||| ||||| ||| | ||||| ||||| || | || |||| ||| | | | |||||
tgtttatacaaatcttctatgttggcttcctattgcaacgga--atccaagtaacttcttgcggt-tgatgactgttccattctccatgcttctttttttcagGGTTTTAGAAAAGTTGATCCAGACCGCTGGGAGTTTGCAAACGAGGGCTTTTTAAGAGGCCAAAAGCAAATACTAAAGAGTATTGTCCGGCGAAAACCTG
upper sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G16820.2 (Arabidopsis thaliana), 3'ss of exon 1
ccttaatttgatttgcactcagctgacaatcgggagagattattttctcagctaacaattatattgcgcc-ctaacgatctcatcggtgccttctta---ccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
| | ||| || | | | || | | || ||| | | | || ||| || | | ||| | || || |||| | |||||| || ||||| |||||||| ||| ||||||||||||||||||| || ||||| ||||| | |||||| || ||||||| ||| ||| || ||||| |
---tgttggcttttcttcttcccctaaattcaagcaacatcgtttcagttcttca-atttgaatttcgatatttatgatagcctctctgtattctgatgtccagGGTTTCAGAAAAGTTGATCCTGACCGATGGGAATTTGCAAATGAAGGATTTCTTAGAGGCCGAAAACAACTACTGAAGAGTATTGTCAGGAGAAAACCTT
upper sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT1G32330.1 (Arabidopsis thaliana), 3'ss of exon 1
ccttaatttgatttgcactcagctgacaatcgggagagattattttctcagctaacaattatattgcgccctaa-cgatctcatcggtgccttcttac--cagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
|| |||||||||| | |||| || | || || | | | || | | || | || ||||| ||||| || || |||||||| ||||| |||||||||||||| ||||| |||||| | ||||| || || || |||| | | || | || | |||||
---gttttagatttgcacttctaaagctgtcggatgaattctttctcattggtcttggtggaatccattttcattccattttgcgtgtcttttcttgatacagGGTTTCAGGAAGGTTGACCCAGATAGATGGGAATTTGCGAATGAAGGTTTTTTAAGAGGTCAGAAGCACTTGCTACAATCAATAACTAGGCGAAAACCTG
upper sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv16s0039g01840.t01 (Vitis vinifera), 3'ss of exon 1
ccttaatttgatttgcactcagctgacaatcgggagagattattttctcagctaacaattatattgcgccctaacgatctcatcggtgccttctt--accagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
| | |||| | ||| || | || || | ||| || | | | || | || | | ||||| ||||| ||||| ||||||||| | |||||||||||||||||||||||||| ||||| |||||||| || |||||| ||| | || | ||| |
--atgcgctattttgttaattgtcttgaatattatttatttgtgtttgtgatcaaaacttagtttctaaggggtagtttttttcttcactttaatcaaacagGGATTTAGGAAGGTGGATCCAGACCGCTGGGAATTTGCAAATGAGGGTTTTCTAAGAGGTCAAAAACACCTTTTGAAGAGTATTAGTAGGCGAAAATCCA
upper sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv02s0012g01810.t01 (Vitis vinifera), 3'ss of exon 1
ccttaatttgatttgcactcagctgacaatcgggagagattattttctcagctaacaattatattgcgccctaa----cgatctcatcggtgccttcttaccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
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-ttttattttgtatgtaatcaaagtctctttgtattctgctgatta--tagtttccctttcttccccatcctattttcctatcttgtcactgtctgcaaac-agGGATTCAGGAAGGTTGATCCAGACCGTTGGGAATTTGCAAATGAGGGATTTTTGAGGGGTCAAAAACACCTATTGAGGAGTATAAATCGGCGAAAACCTGMapped 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|149027368|gb|EE046500.2|EE046500EST: ACTTCAAGCACAGCAACTTCTCCTCGTTCGTCAGGCAGCTCAACACCTAC GGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTT
genomic: ACTTCAAGCACAGCAACTTCTCCTCGTTCGTCAGGCAGCTCAACACCTACgtaagtcacc ... ttcttaccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcagctaacaattatattgcgccctaacgatctcatcggtgccttcttaccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
ccctaac putative branch site (score: 2)
ccttcttacc putative PPT
taacaattatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccttaatttgatttgcactcagctgacaatcgggagagattattttctcagctaacaattatattgcgccctaacgatctcatcggtgccttcttaccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - tgatttg
- - - - - - - - - tcagctg