Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaaatcaatcttgtaattatttgaattttcctaattacattgttaaactacaccttcacatgatatacaaaaactatccttgaccattaatttatatttttgttaccagGGTGAGTATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGCTCTGTTATTGCTGCTGCA
Basic information
species | Glycine max |
transcript | GLYMA17G03920.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 3'ss of exon 11
gtaagaaaatcaatcttgtaattatttgaattttcctaattacattgttaaactacaccttcacatgatatacaaaaactatccttgaccattaatttatatttttgttaccagGGTGAGTATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGCTCTGTTATTGCTGCTGCA
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---------------------------gtatgtgtaataccatttggataatgtgtgcttttaagcatttatgttctattgccctaagatatc--tttctcttattgtt-tcagGGTGAGTATTCATGAGGCCATGGAGCAACAAAGTATCAGTATATCAAAGGCCGGAATTGTCACATCCCTTCAAGCTCGGTGCAGTGTTATTGCTGCAGCA
upper sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 11
gtaagaaaatcaatcttgtaattatttgaattttcctaattacattgttaaactacaccttcacatgatatacaaaaactatccttgaccattaatttatatttttgttaccagGGTGAGTATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGCTCTGTTATTGCTGCTGCA
||| || | | || ||||| || || | | ||| ||| ||| | | ||| |||||| | | || | | ||| ||| |||||| ||||| |||||||| |||||||| |||||||| || ||||||||||| ||||| || ||||||||||| || | ||| |||||||||||| |||
gtatgatataccat-ttgtatttggatgtcctgtgctatttaaatttctgtattac----------------caaaaa-tgtaattttcttctgatt---gttt-------cagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCA
upper sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagaaaatcaatcttgtaattatttgaattttcctaattacattgttaaactac--accttcacatgatatacaaaaactatccttgaccattaatttatatttttgttaccagGGTGAGTATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGCTCTGTTATTGCTGCTGCA
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--------------------------------------gtaacaaaatgcaactaatgatagttacttt-tctgaaggaaatggtgctgac----gatataagtttttgtaaccagGGTGAGTATCCATGAAGCCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCT
upper sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv01s0150g00390.t01 (Vitis vinifera), 3'ss of exon 10
gtaagaaaatcaatcttgtaattatttgaattttcctaattacattgttaaactacaccttcacatgatatacaaaaactatccttgaccattaatttatatttttgttaccagGGTGAGTATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGCTCTGTTATTGCTGCTGCA
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gtaaggaaatgtatgt-gcgtatattttggtacttc--aatcccttgcaaaaatttgtat-catgtga---acaagaa---------------agtttatatcct--ctattagAGTGAGCATCCACGAAGCAATGGAACAGCAGAGTATTAGCATATCAAAGGCTGGGATTGTCACTTCTCTCCAGGCTCGCTGCTCTGTCATTGCTGCTGCA
upper sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ17122 (Selaginella moellendorffii), 3'ss of exon 9
gtaagaaaatcaatcttgtaattatttgaattttcctaattacattgttaaactacaccttcacatgatatacaaaaactatccttgaccattaatttatatttttgttaccagGGTGAGTATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGCTCTGTTATTGCTGCTGCA
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------------------------------------------------------------gtattttaaacgcagggcttacattgtcttactcgggagtattttt----tcagGGTAAGTATACATGAAGCCATGGAGCAGCAAAGTATCAGCATCTCAAAAGCTGGTATAGTAACATCATTGCAAGCTCGTTGCTCTGTGATCGCTGCCGCA
upper sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ31227 (Selaginella moellendorffii), 3'ss of exon 7
gtaagaaaatcaatcttgtaattatttgaattttcctaattacattgttaaactacaccttcacatgatatacaaaaactatccttgaccattaatttatatttttgttaccagGGTGAGTATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGCTCTGTTATTGCTGCTGCA
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------------------------------------------------------------gtattttaaacgcagggcttacaatgtcttactcgggagtattttt----tcagGGTAAGTATACATGAAGCCATGGAGCAGCAAAGTATCAGCATCTCAAAAGCTGGTATAGTAACATCATTGCAAGCTCGTTGCTCTGTGATCGCTGCCGCAMapped 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|193465552|gb|FK431589.1|FK431589EST: AAAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGATCAGGATAG GGTGAGTATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
genomic: AAAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGATCAGGATAGgtaagaaaat ... ttgttaccagGGTGAGTATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
EST:
gi|22523731|gb|BU082542.1|BU082542EST: AAAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGATCAGGATAG GGTGAGTATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
genomic: AAAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGATCAGGATAGgtaagaaaat ... ttgttaccagGGTGAGTATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcacatgatatacaaaaactatccttgaccattaatttatatttttgttaccagGGTGAGTATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGCTCTGTTATTGCTGCTGCA
cattaat putative branch site (score: 3)
tttttgtt putative PPT
accattaatttatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaaatcaatcttgtaattatttgaattttcctaattacattgttaaactacaccttcacatgatatacaaaaactatccttgaccattaatttatatttttgttaccagGGTGAGTATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGCTCTGTTATTGCTGCTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC