Sequence
atgc intronic sequence ATGC exonic sequencegtccctcttttttcttttttcaaaaaatgttatgaccaaaatatctgatatttattcttcctctattatatatgtatttaaatttttttcttttttatagGTGCAAAAGAGGAGAATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAA
Basic information
species | Glycine max |
transcript | GLYMA10G09410.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G09410.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g06200.2 (Oryza sativa), 3'ss of exon 4
----gtccctcttttttcttttttcaaaaaatgttatgaccaaaatatctgatatttattcttcctctattatatatgtatttaaatttttttcttttttatagGTGCAAAAGAGGAGAATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAA
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gttaatatttccttctgtttttttctcatatcctgtttgctaacacgcct-----ttattttg--tcaagcttatatgtatgtaaaatgtttt-------gcagGTACAAAAAAGGCGTATATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAA
upper sequence: GLYMA10G09410.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g33950.1 (Oryza sativa), 3'ss of exon 4
gtccctcttttttcttttttcaaaaaatgttatgaccaaaatatctgatatttattcttcctctattatatatgtatttaaatttttttcttttttatagGTGCAAAAGAGGAGAATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAA
|| | | || | || || ||| | ||| | || || | | ||| ||| ||| | |||| | || || | |||||||||||||| ||||| ||||||| | ||| | || ||||||||||| ||||||||||| | |||||
gtatgggtaaaccccccccctctctctcattttaacagtcatttcttttcgttagttttgctacag-gtttatatatgg-----tttccaacaaaaacagGTTCGGAAACGGCGCATATATGACATAACAAATGTACTGGAAGGAACAGGTTTGATAGAAAAGAAGCTTAAGAACAGAATCCGTTGGAG
upper sequence: GLYMA10G09410.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G333591_T01 (Zea mays), 3'ss of exon 6
gtccctcttttttcttttttcaaaa-aatgttatgaccaaaatatctgatatttattcttcctctattatat-atgtatttaaatttttttcttttttatagGTGCAAAAGAGGAGAATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAA
| | || | | | | || | | || || || | || | | | || | | | || | || | | ||||||| |||| || || ||| | ||||||||||| ||||||||| | ||||| || || || || ||||||||||| ||||||| || | ||||||
gatgatattgatgttgactagaggttggtgctttccttttggtaccttg-atccagtcatggtttcttttgttaaacatatgcatatatagctttttt-cagGTACAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAGAACAACATCCGTTGGAA
upper sequence: GLYMA10G09410.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G829408_T01 (Zea mays), 3'ss of exon 6
--gtccctcttttttcttttttcaaaa-aatgttatgaccaaaatatctgat--atttatt-cttcctctattatatatgtatttaaatttttttcttttttatagGTGCAAAAGAGGAGAATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAA
| | || | | | | || | | || |||| | | || ||| | | ||| | || | || || ||| | |||| || || ||| | ||||||||||| ||||||||| | ||||| || || || || ||||||||||| ||||||| || | ||||||
cagatgatattgatgttgactagaggttggtgctttccttttggtacttgatccagtcatggtttcttttgttaaacatatgcgtatatagctttttc------agGTACAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAGAACAACATCCGTTGGAA
upper sequence: GLYMA10G09410.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g02510.t01 (Vitis vinifera), 3'ss of exon 4
gtccctcttttttcttttttcaaaaaatgttatgaccaaaatatctgatatttattcttcctctattatatatgtatttaaatttttttcttttttatagGTGCAAAAGAGGAGAATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAA
| ||| |||||| | | || | || | | |||| ||| || ||| | |||||| | |||| | | |||| || |||||| | |||||||||||||| |||||| ||||||| |||||||||||||||||||||||||||||||| || | |||||
--------gtgttcatttttctatttaagt--------acatgtataatataaattac------atgctattttaatttaaggtcttttatacaa-acagGTTCAGAAGAGGCGGATATATGACATAACAAATGTTCTGGAAGGAATTGGTCTCATTGAAAAGAAGCTCAAGAACAGGATCCGCTGGAA
upper sequence: GLYMA10G09410.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S364_42V6.1 (Physcomitrella patens), 3'ss of exon 4
-gtccctcttttttcttttttcaaaaaatgtta--tgaccaaaatatctgatatttattcttcctctattatatatgtatttaaatttttttcttttttatagGTGCAAAAGAGGAGAATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAA
|| || | | | | | | || | ||| |||| | | |||| || | | | || ||| || || | | | |||| |||| |||||||| ||||| |||||||| || |||||||||||||| || || | |||||||||||||| || || | || |||||
tgtgactgtgtctgagagagggagagagagtgagttgatttaaatttattatatctagtat-ctactggctgata-gtgttaggaatccgtggttttac-cagGTACAAAAGAGAAGAATTTATGACATCACCAATGTTTTGGAAGGGATCGGGTTAATTGAAAAGAAGCTGAAAAATCGGATTAGATGGAA
upper sequence: GLYMA10G09410.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S97_96V6.1 (Physcomitrella patens), 3'ss of exon 5
gtccctcttttttcttttttcaaaaaatgttatgaccaaaatatctgatatttattct--tcctctattatatatgtatttaaatttttttcttttttatagGTGCAAAAGAGGAGAATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAA
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aataatgtgtttgtatttctttaaaaatgcattaactcatctttcatatttacattctgatggcctacaatgctgggaattttactatttatttcatca--gGTACAAAAGAGAAGAATATATGACATCACCAATGTGTTAGAAGGGATTGGGTTAATTGAGAAGAAGCTGAAAAACCGGATTAGATGGAAMapped 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|15663288|gb|BI700659.1|BI700659EST: ATGCAGAGGGTGGTATTCTTGACCTAAATAAAGCAGCAGAAACTTTGGAG GTGCAAAAGAGGAGAATATATGACATAACTAATGTTTTGGAAGGCATTGGT
genomic: ATGCAGAGGGTGGTATTCTTGACCTAAATAAAGCAGCAGAAACTTTGGAGgtccctcttt ... ttttttatagGTGCAAAAGAGGAGAATATATGACATAACTAATGTTTTGGAAGGCATTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatatttattcttcctctattatatatgtatttaaatttttttcttttttatagGTGCAAAAGAGGAGAATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAA
atctgat putative branch site (score: 4)
tttttttcttttttat putative PPT
tctattatatatgtat 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
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gtccctcttttttcttttttcaaaaaatgttatgaccaaaatatctgatatttattcttcctctattatatatgtatttaaatttttttcttttttatagGTGCAAAAGAGGAGAATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC