Sequence
atgc intronic sequence ATGC exonic sequence...gtgcttaaatttaaaacaactgaaaattacagttggtacctgtaactatcagctaattctagcaatctgttatatccttaacatcacttgttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
Basic information
species | Glycine max |
transcript | GLYMA18G50760.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
gtgcttaaatttaaaacaactgaaaattacagttggta----cctgtaactatcagctaattctagcaatctgttatatccttaacatcacttgttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
| | | | || | || ||| | ||| | | | || | || | ||| | | | |||| | || || | | | ||||||||||||||||||||||| ||||||||||| |||||||| |||||||| ||||| || |||||||| || || ||||| || |||||||| || ||||
---atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttcttaacaaaaataaaat-ctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
upper sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g54750.1 (Oryza sativa), 3'ss of exon 3
-gtgcttaaatttaaaacaactgaaaattacagttggtacctgtaactatcagctaattctagcaatctgttatatccttaacatcacttgtttt--ttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
|| | | | || ||| | | | | | | | | | | | | || || ||||||| | | | |||||||||||||||||||||| |||||||||||||||||||| |||||||| ||||| | || ||||| || || || || || || ||||| || ||||
taagcatcgtgatggcgttatgagaagttaaatt--atgttttaagtcttataccagaaatttctctttattg-attcttaacaagataaactctacttgcagTGACATGGAATGTGACCTGCACATACTCACAATTTCTTGCTCAGAAGACTCCAACCTGTTGTGTATCTCTCTCGTCATTTTACAATGACACAATTGTGAA
upper sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g30260.1 (Oryza sativa), 3'ss of exon 3
gtgcttaaatttaaaacaactgaaaattacagttggtacctgtaactatcagctaattctagcaatctgttatatccttaacatcacttgttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
| || | | | || | | | || | |||| | | | | |||| || |||||||||||||| |||||||||||||||||||| || || ||| | ||||| | | |||| |||| ||||| ||||||||||| || || ||||| || | |||
---------------------gtaagtcatt-tcagtgttttt---tgtctttctggcgtcacaat-tatgacaccctt----tcttcctttttttgcagTGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTCCAACTTGTTGTGTTTCACTTTCATCGTTTTACAATGAGACAATAGTTAA
upper sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g41310.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------------------gtgctta-aatttaaaacaactgaaaattacagttggtacctgtaactat-cagctaattctagcaatctgttatatccttaacatcacttgttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
| ||||| ||| || |||| | | | | | ||| | | ||| | || | || ||| ||| || | || | | | || |||| ||||||||||||||||||||| |||||||| ||||| || | || || | | |||| | ||||| || || || || ||||| || ||||||||| | |||
gtaagatttttttctgaagtttccatgatcttagtatttgccgtgcaaagtagttcagggatgagcttacaatctattgcaac--agattcagaattgtt-cttgtttcgatactgccttttcgtgca-tcatcggtgacc---gcttgatttcttttgtgcagTGACATGGAATGTGACTTGCACATATTCACAGATTGTCGCGCAAAGATCTCCGACGTGCTGCGTTTCGCTCTCGTCTTTTTACAATGATACCATAGTTAA
upper sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g35460.1 (Oryza sativa), 3'ss of exon 3
---gtgcttaaatttaaaac--aactgaaaattacagttggtacctgtaactatcagctaattctagcaatctgttatatccttaacatcacttgttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
| ||| || | | | | || | | ||| || |||| || | |||| | | | || | || | | | || |||||||||||||||||| ||||||||||| |||||||| || || || ||| || |||||||| || || || || ||| | ||||| | ||||
ataggacttgttgtttgttttgagttctatagtagaaaaaattcctatat---tcag-tactactagtagtacttcttaacaaaaaggaaatct-ctattcacagTGACATGGAATGTGATCTGCACATACTCCCAATTTCTTGCACAAAAGGTTCCATCCTGCTGTGTTTCTCTCTCGTCGTTCGACAATGACAAAACTGTTGA
upper sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
gtgcttaaatttaaaacaactgaaaattacagttggtacctgtaac--tatcagctaattctagcaatctgttatatccttaacat-cacttgttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
| ||| | | | | | | ||| || | | || ||| | | | | ||||||| || | || | ||||||||||||||||||||| |||||||| || |||||||| |||||||| ||||| || |||||||| || || ||||| || |||||||| || ||||
---ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgtctatattttatagcactgagggttcttaacagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
upper sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G826714_T01 (Zea mays), 3'ss of exon 3
gtgcttaaatttaaaacaactgaaaattacagttggtacctgtaactatcagctaattctagcaatctgttatatccttaacat---cacttgttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
| | | || | | | |||| || | | || | || | ||| | | | | ||||||| || | || | ||||||||||||||||||||| |||||||| || |||||||| |||||||| ||||| || |||||||| || || ||||| || |||||||| || ||||
ctaatcgcagatagtcctaggaagaattcca--tacaagttgca-cttttgtctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTATCATCGTTTTATAATGACACAATTGTGAA
upper sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G009154_T01 (Zea mays), 3'ss of exon 2
gtgcttaaatttaaaacaactgaaaattacagttggtacctgtaac--tatcagctaattctagcaatctgttatatccttaacat-cacttgttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
| ||| | | | | | | ||| || | | | ||| | | | | | |||| || || | || | ||||||||||||||||||||| |||||||| || |||||||| |||||||| |||| || |||||||| || || ||||| || |||||||| || ||||
---ttctaatcacagatagtcttaggaaaatttccatacaagttgcagttttgtctatattttatagcattgagagttcttatcagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCTGTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
upper sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G826714_T02 (Zea mays), 3'ss of exon 3
gtgcttaaatttaaaacaactgaaaattacagttggtacctgtaactatcagctaattctagcaatctgttatatccttaacat---cacttgttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
| | | || | | | |||| || | | || | || | ||| | | | | ||||||| || | || | ||||||||||||||||||||| |||||||| || |||||||| |||||||| ||||| || |||||||| || ||
ctaatcgcagatagtcctaggaagaattcca--tacaagttgca-cttttgtctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT------------------------------
upper sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G02210.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgcttaaatt-taaaacaactgaaaattacagttggtacctgtaactatcagctaattctagcaatctgttatatccttaacatcacttgttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
||| || | |||| ||| | | | ||| | | | | | | ||| | | || | | | | ||||||| |||||||| || ||||||||||| || || | ||||||||||| || |||||||||| || |||||||| || ||||| | || | ||| |
----gtaagttactcagttcttgaactctaccaa-aacaaatttgacttttgagtgaaatgaaaactgagttttggcttt--tctttttctgctgtgacagTGACTTGGAATGTAACTTGCACATACTCGCAGTTCTTAGCTCAGAAAACACCAACTTGCTGTGTATCTCTTTCATCGTTTTATAACAAGACAATAGTTTC
upper sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 3
---gtgcttaaatttaa-aacaactgaaaattacagttggtacctgtaactatcagctaattctagcaatctgttatatccttaacatcacttgttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
|| | | | |||| || |||| ||| || | | | | | | |||| || | ||| ||| | || | | |||||||| |||||||| || ||||| || |||||||| ||||||||||| || || | || ||||||||| | ||||| ||||||||| | || | || |
aggatggcaagacacattgacaatggataatttgtgttcttaa-tatg-catttaaagagttctcaagatttaactaatc--taatcttcctgtcctatggcagTGACTTGGAATGTTACTTGCACGTATTCACAATTCCTGGCTCAGAAGACGCCTACATGTTGTGTCTCATTGTCATCGTTCTATAATAACACTATAGTATC
upper sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
-gtgcttaaatttaaaacaactgaaaattacagttggtacctgtaactatcagctaattctagcaatctgttatatccttaacatcacttgtttttt--gcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
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agggagtgattcttaaagg--caatttttgtcttccctaattaaaaatttgagctattacccataaa-tgtactgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACCMapped 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|298182947|gb|HO028160.1|HO028160EST: ACCCACTAAATTCATTACTTCAGACAAAAGGAGAGTGACCCAAGCACTGA TGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTC
genomic: ACCCACTAAATTCATTACTTCAGACAAAAGGAGAGTGACCCAAGCACTGAgtaagtcata ... ttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctatcagctaattctagcaatctgttatatccttaacatcacttgttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
ccttaac putative branch site (score: 3)
cttgtttttt putative PPT
ttgtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcttaaatttaaaacaactgaaaattacagttggtacctgtaactatcagctaattctagcaatctgttatatccttaacatcacttgttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC
gtgctta
- - - - - - aaaacaa
- - - - - - - - - - - - - - - - - - -acctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatcac