Sequence
atgc intronic sequence ATGC exonic sequence...tgtaggtactattgttatgttggaaagtctgtattcttgtcattggtctgtgttccttttggccttgacatgccatctgaacccatgttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACCGAGTATCTGGGATCAGCTGCATTTAGC
Basic information
species | Glycine max |
transcript | GLYMA16G34510.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G34510.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g51020.1 (Oryza sativa), 3'ss of exon 2
----------------------------------------------tgtaggtactattgttatgttggaaagtctgtattcttgtcattggtctgtgttccttttggccttgac-atgccatctgaacccatgttttgttgct----------cagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACCGAGTATCTGGGATCAGCTGCATTTAGC
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gtgctctttttctggtccttaattacttggcatttctttattagttcatttgtattaaaatgatacttggtatcatgc-ttggtgtttgcgtttgttaatttgtttatctctaacgatattttttaactccattatatcctgctgacaatataacagAACTGGTTTTGAAGAAGACAAAAATTTCCATGTTGTTCTCAACTCTGTCATTGCTGGACGTTACCATGTCACAGAATATCTGGGTTCAGCAGCATTCAGT
upper sequence: GLYMA16G34510.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G181002_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------------------tgtaggtactattgttatgttggaaagtctgtattcttgtcattggtctgtgttccttttggccttgacatgccatctgaacccatgttttgttgct---cagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACCGAGTATCTGGGATCAGCTGCATTTAGC
|| || | | || ||| || | | | | | | || || | | | || | ||| | || | | |||| | ||||||||||||||| || ||||| ||||||||||||||| | |||||||| | |||||||| |||||||| | |||||| |||| |||||||| || |||
gtattttctttaaatgattgttccatctgttaatcttgttaaagcataaaaaaatgatatggtaatttccagttatctattgtccttgtgtgcctgtgttcacagtgtggcacctacgccgtatttttaaaagatattttatatcttctaacaccgtctcctgttaattaacagAACTGGCTTTGAAGAAGACAAAAATTTCCATGTTGTTCTCAATTCTGTCATTGCTGGGCGTTATCATGTATCAGAGTATTTGGGGTCAGCTGCTTTCAGC
upper sequence: GLYMA16G34510.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G015073_T01 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------tgtaggtactattgttatgttggaaagtctgtattcttgtcattggtctgtgttccttttg---gccttgacatgccatctgaacccatgttttgttgct---cagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACCGAGTATCTGGGATCAGCTGCATTTAGC
| || || | || | | | | |||| ||| | | || | |||| | || ||| | || | | || | ||||||||||||||| || ||||| || |||||||||||| | |||||||| | |||||||| |||||||| | |||||| |||| ||||||||||| |||
gtaatgcatttaaatgtttgtcccatattttaatcttactaaagcataaaaaatgatgtggtgattttcagttatc--tattgtccttgtgtgcctgtgttcacagtgtggcacttaaacctttttataaagtattttgtgtattctaacattatctcctattaattatcagAACTGGCTTTGAAGAAGACAAAAACTTCCATGTTGTTCTCAATTCTGTCATTGCTGGGCGTTATCATGTATCAGAGTATTTGGGTTCAGCTGCATTCAGC
upper sequence: GLYMA16G34510.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------tgtag-gtactattgttatgttggaaagtctgtattcttgtcattggtct-gtgttccttttggcc-ttgacatgccatctgaacccatgttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACCGAGTATCTGGGATCAGCTGCATTTAGC
||| |||| | || | | | | | | |||| ||| ||| || | || || | || | | | || |||||| ||| ||||| ||||||||||| ||||| |||||||| ||||| |||||||| | ||||| || || |||||||| ||| |||| |||||||| || ||||||
gtctgttcccttacaatatcgtggtttattatgtattaaatgatgtttcgtacacattttgtttagaagggggatgaagtctgtcccgaatcttgtgaaccctcaggaaatttatttgtttcttctatttgtcttctgttgcccagGACTGGTTTTGAGGAGGATAAGAACTTCCATGTGGTTTTGAATTCTGTCATTGCTGGTCGTTACCATGTCACTGAGCATCTTGGATCAGCAGCTTTTAGC
upper sequence: GLYMA16G34510.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 8
tgtaggtactattgttatgttggaaagtctgt----attcttgtcattggt--ctgtgttccttttggccttgacatgcc-atctgaacccatgttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACCGAGTATCTGGGATCAGCTGCATTTAGC
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-------gccagtttcaagttcacaacttttccaccagttttgccattgggaactttgcttgttctaacaggaagtttcttatctcaatttctgttttgtggtgcagAACTGGGTTTGAGGAGGACAAAAACTTCCATGTTGTTTTAAATTCAGTCATAGCTGGGCGCTATCATGTTACCGAGTATCTTGGGTCAGCTGCATTCAGCMapped 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|24137018|gb|BU927528.1|BU927528EST: AGGAATTTGAAACCTTCAATCTAAAGATTGTGCACAGGAAAAACAG AACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACT
genomic: AGGAATTTGAAACCTTCAATCTAAAGATTGTGCACAGGAAAAACAGgcatgtctta ... tgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtctgtgttccttttggccttgacatgccatctgaacccatgttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACCGAGTATCTGGGATCAGCTGCATTTAGC
ccttgac putative branch site (score: 4)
ttttgtt putative PPT
atgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtaggtactattgttatgttggaaagtctgtattcttgtcattggtctgtgttccttttggccttgacatgccatctgaacccatgttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACCGAGTATCTGGGATCAGCTGCATTTAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - tgttatg
- - - - - - - - - - - - - - -tgtattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttt