Sequence
atgc intronic sequence ATGC exonic sequencegttgggttgcattaaaatttgaaaaattcaatattattctgttatttataactttgtactctatctttctaattgtctgccaaaaatagggtactgattctcatctaacctgtttattgtgaaatgttgtattaacttttacaagcatgctcccttgtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCGTTTGCTGAGAGGAGGGAGTTTGACAAAATTC
Basic information
species | Glycine max |
transcript | GLYMA14G06340.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 12
gttgggttgcattaaaatttgaaaaattcaatattattctgttatttataactttgtactctatctttctaattgtctgccaaaaatagggtactgattctcatctaacctgttt-attg--tgaaatgttgtattaacttttacaagcatgctcccttgtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCGTTTGCTGAGAGGAGGGAGTTTGACAAAATTC
||| | | || || | ||| ||| | ||| | | || | | ||||||| | || || | |||| ||||| | ||| ||| || |||||||||||||||||||||||||| | |||||||| || || || || || || || ||||||||||| || |||||||| || ||||| |||||||| || |
-----------------------------------------------gtaaaatgg-gtgttaagttgtttgttgattgc---acatatcgattttgttacactgtgtcctgtttgactgtctggattgtt-cattaattgatacctgcactctttggtgtagACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 12
gttgggttgcattaaaatttgaaaaattcaatattattctgttatttataactttgtactctatctttctaattgtctgccaaaaatagggtactgattctcatctaacctgttt-attg--tgaaatgttgtattaacttttacaagcatgctcccttgtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCGTTTGCTGAGAGGAGGGAGTTTGACAAAATTC
||| | | || | | | | ||| ||| | ||| | | || | | ||||||| | || || | |||| ||||| | ||| ||| || |||||||||||||||||||||||||| | |||||||| || || || || || || || ||||||||||| || |||||||| || ||||| |||||||| || |
-----------------------------------------------gtaaaatgggtcttaagttgtttg-ttgattgc---acatatcgattttgttacactgtgtcctgtttgactgtctggattgtt-cattaattgatacctgcactctttggtgtagACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
gttgggttgcattaaaatttgaaaaattcaatattattctgttatttataactttgtactctatctttctaattgtctgccaaaaatagggtactgattctcatctaacctgtttattgtgaaatgttgtattaacttttacaagcatgctcccttgtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCGTTTGCTGAGAGGAGGGAGTTTGACAAAATTC
|| | | | | || | | || | ||| | | | | | | | | | || | | || |||| | || || | || || | | || |||||||||||||||||||||| | |||||||| ||||| ||||| || || || |||||||||||||| |||||||| |||||||||||||||||||| |
----------------------------------------gtaagatg-ggtcctatgctgt-ttttattgatt--ttactgtattttgttaaattacatttatttgtcttggttatcgctaatcatttcttgtaccctttgatgtat----------agACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
gttgggttgcattaaaatttgaaaaattcaatattattctgttatttataactttgtactctatctttctaattgtctgccaaaa-atagggtactgattctcatctaacctgtttattgtgaaatgttgtattaacttttacaagcatgctcccttgtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCGTTTGCTGAGAGGAGGGAGTTTGACAAAATTC
| ||| | | | | | | | | ||| | | ||| ||| | | | | ||||| |||| | ||| | | | || ||||||||||||||||||||||||| | |||||||| || || || || || || || |||||||||||||| |||||||| ||||||||||||||||| | |
---------------------------------------------------tgtcataccgtgtttgttgatgcatggatcttactatactttgccaatttacattca-cttatgtattg---gttgtt-tgctaagtgt-----gtgcacttttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 6
gttgggttgcattaaaatttgaaaaattcaatattattctgttatttataactttgtactctatctttctaattgtctgccaaaaatagggtactgattctcatctaacctgtttattgtgaaatgttgtattaacttttacaagcatgctcccttgtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCGTTTGCTGAGAGGAGGGAGTTTGACAAAATTC-----------------
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----------------------------------------------------------------------------------------------caatttacattca-cttatgtattg---attgtt-tgctaagtgt-----gtgcacttttatgtagactgtggacaatgatcttgcactgaaaatatacataaaggctagGGC-ACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 12
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 12
gttgggttgcattaaaatttgaaaaattcaatattattctgttatttataactttgtactctatctttctaattgtctgccaaaaatagggtactgattctcatctaacctgtttattgtgaaatgttgtatta-acttttacaagcatgctcccttgt--agACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCGTTTGCTGAGAGGAGGGAGTTTGACAAAATTC
|| || | ||| |||| ||| ||| | | || | | || || || | || || | || | |||||||||| ||||| |||||| |||||||||| |||||||| ||||||||||||||||| ||||| || ||||| ||| | |||||||||||||||||
-------------------------------------------------------------------------------gtaatcttaaaatgaccattttcatttaaagtgtctcctatgggcttctttagtatgctgtaacggtaatattttctgattcagACTGTGGATAATGACCTTGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATAT
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 12
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 12
gttgggttgcattaaaatttgaaaaattcaatattattctgttatttataactttgtactctatctttctaattgtctgccaaaaatagggtactg-attctca---tctaacctgtttattgtgaaatgttgtattaacttttacaagcatgctcccttgtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCGTTTGCTGAGAGGAGGGAGTTTGACAAAATTC
|| | |||| | | | |||| | | | | ||| | | || |||||| | || | | || || |||||||||| |||||||| ||| | |||||||| |||||||| | || |||||||||||||| || || ||||| || || ||||||||||||||||| |
--------------------------------------------------------------------------gtaatcttgaaatggacgattttattcaaaatgtgtgatatgtctcctatggtgtgttgtgacgat------aaacct-ttctgttccagACTGTGGATAATGATCTCGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATAC
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 12
gttgggttgcattaaaatttgaaaaattcaatattattctgttatttataactttgtactctatctttctaattgtctgccaaaaatagggtactgattctc---atctaacc--tgtttattgtgaaatgttgtattaacttttacaagcatgctccctt-gtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCGTTTGCTGAGAGGAGGGAGTTTGACAAAATTC
| ||| | | |||| || | | | |||| || | ||| || | | | |||||| | | | || | | || || || ||| | ||| || | |||| | | || || || | || |||| | || |||||||||||| | ||| ||||| | ||||||||||| ||||| ||||| ||||| ||||||||||| || ||||||||| | ||||||||||||||||||
----gtttgaaatgcaattggaga---tgattattttttgtccacttaagacaattcttgttgggatgctaatt-tgagtttattttattatttttatcctgctaatttaaatgatttttttttttaaatataattttgacattgaaaaccatgttttttttgtagACTGTGGATACTGACCTTGCACTCAAAATATATATTAAAGCGAGAGCAACTCCGAAAGTTGTTGCAGCCTTTGCTGAGCGTCGGGAGTTTGACAAAATTCMapped 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|20815168|gb|BQ299646.1|BQ299646EST: TGGCAGAGGACAAGCTTGAATGCAGTGAGGAGCTAGGAGATCTCGTTAAG ACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACT
genomic: TGGCAGAGGACAAGCTTGAATGCAGTGAGGAGCTAGGAGATCTCGTTAAGgttgggttgc ... tcccttgtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taacctgtttattgtgaaatgttgtattaacttttacaagcatgctcccttgtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCGTTTGCTGAGAGGAGGGAGTTTGACAAAATTC
tattaac putative branch site (score: 1)
tgctccctt putative PPT
ttgtattaactttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgggttgcattaaaatttgaaaaattcaatattattctgttatttataactttgtactctatctttctaattgtctgccaaaaatagggtactgattctcatctaacctgtttattgtgaaatgttgtattaacttttacaagcatgctcccttgtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCGTTTGCTGAGAGGAGGGAGTTTGACAAAATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG