Sequence
atgc intronic sequence ATGC exonic sequence...tatgaaattttttaggctcactttatctgtctctgtctctatttatgctttgaaatataccagagtcgtttaaaatctccaacattgcattaattctcagGGTGAAGAATACAAGTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAG
Basic information
species | Glycine max |
transcript | GLYMA16G05580.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G05580.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os09g33530.1 (Oryza sativa), 3'ss of exon 10
-------------------------------------------------------------------------tatgaaattttttaggctcactttatctgtctctgtctc-tatttatgctttgaaatataccagagtcg-tttaaaatctccaacattgcattaattctcagGGTGAAGAATACAAGTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAG
|| | | | | | || ||| ||| | | || || || | || | || | || || | |||| | | |||||| || || || ||||| || ||||| || || || || ||||| ||||||||| |||| |||||||| | |||| |||| ||||| |||||||||||||
gtagcaacagttttggcagatggatcatagagccagtgttatcatgaaatcagtttgaatttggcagatagatcatagagtcagtgatac-catgaaatcaatctgaatttggcatatagaacctgtgagatcatgaaatcaatctactgactagaggattg-gctgttcttcagGGAGAGGAGTATAAGTTGTTTTGGCCAGAGCAGTCTGAATTTGTGAGGATGGCATCAAGGTTTGGAGCAACAATAATACCATTTGGAGTAGTTGGAGAAG
upper sequence: GLYMA16G05580.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G26840.1 (Arabidopsis thaliana), 3'ss of exon 10
tatgaaattttttaggctcactttatctgtctctgtctctatttatgctttgaaatataccagagtcgtttaaaatctccaacattgcattaattctcagGGTGAAGAATACAAGTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAG
||| || | | | ||||| || | | | | | || ||| ||| |||| | || | | | |||| |||| |||||||||||||||||| | || ||||| |||| ||||||||||| || | ||| | | ||||||||||||||| || ||||||||||| ||||||||||
-gtgatatatagtttgtaaactttttccgggtttctgcattcttgaaacttgt--tattttagaggctttaatgaaca--aacaa------aatttgcagGGTGAAGAATACAAGCTGTTTTGGCCAGAACGGTCCGAGTTTGTGAGAGTTGCATCTAAATTTGGAGCCAAAATTGTTCCTTTTGGTGTTGTTGGAGAAG
upper sequence: GLYMA16G05580.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G41120.1 (Arabidopsis thaliana), 3'ss of exon 10
tatgaaattttttaggctcactttatctgtctctgtctctatttatgctttgaaatataccagagtcgtttaaaatctccaacattgcattaattctcagGGTGAAGAATACAAGTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAG
| | | | | | | || | | | | ||| || ||| | || || || || |||| | ||||||||||||||||||||||| ||||| ||||| || |||||||||||||| ||| | | ||||||||| ||||| | |||||||| || ||||||||||
----------------gtgattatgtat-tttccatattttccttcatttta----atttttgaggcttt----atatctaaagacacattttataacagGGTGAAGAATACAAGTTATTTTGGCCAGAACATTCGGAGTTTGTAAGGATAGCATCTAAATTTGGAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAG
upper sequence: GLYMA16G05580.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G26820.1 (Arabidopsis thaliana), 3'ss of exon 12
--tatgaaattttttaggc-tcactttatctgtctctgtctctatttatgctttgaaatataccagagtcgtttaaaatctccaacattgcattaattctcagGGTGAAGAATACAAGTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAG
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gttatgttataattaatatattgttgcgtggtgacctttttcggtttctacaattttggatattagtgttttggaggttaacatgtaaagagagacttcacagGGTGAAGAATACAAGCTGTTTTGGCCAGAACAATCCGAGTTTGTGAGAGTTGCATCTAAATTTGGAGCGAAAATCGTTCCTTTCGGTGTTGTTGGAGAAG
upper sequence: GLYMA16G05580.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G41130.2 (Arabidopsis thaliana), 3'ss of exon 10
tatgaaattttttaggctcactttatctgtctctgtctc-tatttatgctttgaaatataccagagtcgtttaaaatctccaacattgcattaattctcagGGTGAAGAATACAAGTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAG
| || | | |||| ||||| ||| | || || |||| | | || |||| | |||||||||| ||||||||| || ||||| ||||| || ||||||||||||| ||| | | ||||||| | ||||| | |||||||| || ||||| ||||
---------------------gtaatgattagatatctcatatttggccttcgttttaactttgaagcgtt----acatagaatgacacatt--tctacagGGTGAAGTATACAAGTTGTTTTGGCCAGAACATTCAGAGTTTGTAAGGACCGCATCTAAATTTGGAACAAAAATCATTCCTTTTGGGGTTGTTGGTGAAG
upper sequence: GLYMA16G05580.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv14s0068g01430.t01 (Vitis vinifera), 3'ss of exon 10
tatgaaattttt-taggctcactttatctgtctct-gtctctatttatgctttgaaatataccagagtcgtttaaaatctccaacattgcattaattctcagGGTGAAGAATACAAGTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAG
| | || | | | | | || || | || || | | | ||| | | | ||| ||| ||| | ||| | | | ||||||| ||||||||||| || ||||| |||||||| |||||||| | || || || || |||||||||||||| |||| ||||| || ||||||||||
-aaaatatgtgtgcatgtatatttcatagccatgaagtagacatgtcggggtcacaattttaaaataccttttgcaatactcaattgttcat-attgtttagGGTGAGGAATACAAGTTGTTTTGGCCAGAACAATCTGAGTTTGTCCGAATTGCGGCTAGGTTTGGAGCCAAAATTATACCCTTTGGAGTTGTTGGAGAAG
upper sequence: GLYMA16G05580.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv14s0068g01440.t01 (Vitis vinifera), 3'ss of exon 10
-----------------------------------------------------------------------------------tatgaaattttttaggct----cactttatctgtctctgtctct-----atttatgctttgaaat-----ataccagagtcgttt--aaaatctccaacattgcattaattctcagGGTGAAGAATACAAGTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAG
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gtaacattttagtaattacattctacattgaagtacattgctctggataaaagtgtttttttttttcctttaggttcctacaacaaaaattcatataaacatgtgcattatatgtgtgcatggctgtgaaagaaatatgccttagaatttgaagtattaaactcttttttgcaacacccaactgtttac-attgtccagGGTGAGGAATACAAGTTGTTTTGGCCAGAATCATCTGAGTTTATCCGAATGGCGGCTAGATTTGGAGCCAAAATTGTACCCTTTGGGGTGGTTGGAGAAGMapped 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|15813571|gb|BI785846.1|BI785846EST: CTCATGTCCTATTATATCCTGGAGGGATACGCGAGGCTTTTCATAGGAAG GGTGAAGAATACAAGTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATG
genomic: CTCATGTCCTATTATATCCTGGAGGGATACGCGAGGCTTTTCATAGGAAGgtaaatctca ... taattctcagGGTGAAGAATACAAGTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATG
EST:
gi|254346772|gb|GR856494.1|GR856494EST: CTCATGTCCTATTATATCCTGGAGGGATACGCGAGGCTTTTCATAGGAAG GGTGAAGAATACAAGTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATG
genomic: CTCATGTCCTATTATATCCTGGAGGGATACGCGAGGCTTTTCATAGGAAGgtaaatctca ... taattctcagGGTGAAGAATACAAGTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctttgaaatataccagagtcgtttaaaatctccaacattgcattaattctcagGGTGAAGAATACAAGTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAG
cattaat putative branch site (score: 3)
ttctc CT-rich tract
tttaaaatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatgaaattttttaggctcactttatctgtctctgtctctatttatgctttgaaatataccagagtcgtttaaaatctccaacattgcattaattctcagGGTGAAGAATACAAGTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA