Sequence
atgc intronic sequence ATGC exonic sequencegttagaaaataaactcgacttagtttttcccctaagcaattgaaacatcttttataggtattaattattatctttttgtagGATGACCCAAATAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
Basic information
species | Glycine max |
transcript | GLYMA11G00920.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G00920.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os07g07974.1 (Oryza sativa), 3'ss of exon 6
gttagaaaataaactcgacttagttt---ttcccctaagcaattgaaacatcttttataggtattaatta--ttatctttttgtagGATGACCCAAATAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
||| | | |||| | | | ||| | | || | | | | || || | | ||| |||| || || || || |||||||||||||| ||||| || ||||||||||| ||||| || |||||||| || |||||||| |||||||| ||||||
-gtaggcgctttttgctggatagtctgtactacttctagccctcatttccatttatgtggtgctgaaatacttcaataaattgcagGAAGATCCTAACAACACTCCAGCTTCAGCTCGACATAAGAGAGGATGCAATTGCAAGAAGTCAAGCTGTCTTAAGAAATACTGTGAATGCTATCAG
upper sequence: GLYMA11G00920.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G701689_T01 (Zea mays), 3'ss of exon 6
gttagaaaataaactcgacttagtttttcccctaagcaattgaaacatcttttataggtattaattattatcttt----ttgtagGATGACCCAAATAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
|| | | ||| ||||| | | || | || | | | | | || || | || ||||| |||||||| | | ||||||||||| |||||||| || |||||||| |||||||| ||||| || || || ||||| ||||| |||||||||| ||||
---gtaagagacact-aacttattgtatctgagtacttcccttaatcttgtctgttgctaata-tcatcatcttcaatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAG
upper sequence: GLYMA11G00920.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G322090_T01 (Zea mays), 3'ss of exon 7
gttagaaa-ataaactcg----actt-agtttttcccctaagcaattgaaacatcttttataggtattaattattatctttttgtagGATGACCCAAATAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
|| ||| | | |||| |||| ||| ||||| ||| | ||| ||| || ||| | | | | ||||||| | ||||||||||| |||||||| || |||||||| |||||||| ||||| || || || ||||| ||||| |||||||||| ||||
gtaagagacactaacttattgtacttgagtatttcctttaatc--ttg-----tctgttgctaatatcattgtcttcaatactgtagGACTTTTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAATTGCAAGAAGTCGTCGTGTCTAAAAAAATACTGTGAATGTTTTCAG
upper sequence: GLYMA11G00920.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G153754_T01 (Zea mays), 3'ss of exon 6
--------------------gttagaaaataaactcgactta-gtttttcccctaagcaattgaaacatcttttataggtattaattattatctttttgtagGATGACCCAAATAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
||| || | | | | | || || | | | | | | | | | ||| || || | | |||| || || || || ||||| ||||| || || ||||| ||||||||||| || || || |||||||| || |||||||| |||||||| || |||
gtatggcgttgcgtacttctgttggagattgagatgtatgtacgtgtgttggccatttactcccagaccgtggtgcttacatt--ctacaatgaaatcgcagGAAGATCCTAACAACACTCCGGCTTCGGCTCGTCACAAGAGAGGATGCAATTGTAAGAAGTCAAGCTGTCTCAAGAAATACTGTGAATGCTACCAG
upper sequence: GLYMA11G00920.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 5
gttagaaaataaactcgacttagtttttcccctaagcaattgaaacatctt--ttataggtatta-attattatctt--tttgtagGATGACCCAAATAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
|| || | | | | |||| || || | ||||| || || ||| | | |||| | | ||||||| ||| |||||||||||||| || || || ||| | || ||||||||||| ||||||| ||| || |||||||| |||||||| ||||||
gtaggattcttttccccgtcctttgattcctctgcatcatccatctatcttgcttgaagttataataatattgtaatgacacacagGATGATGCAAGCAAAACTCCAGCTTCTGCGCGCCATAAACGTGGCTGCAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
upper sequence: GLYMA11G00920.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G22760.1 (Arabidopsis thaliana), 3'ss of exon 6
----gttagaaaataaactcgacttagtttttcccctaagcaattgaaacatcttttatagg-tattaattattatctt--tttgtagGATGACCCAAATAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
|| | | || ||| || | ||| | | | | | || | ||| ||| || | | || || |||| || ||| |||||||||||||||||| ||||||||| |||| || |||||||| ||||||| ||| || |||||||| |||||||| ||||||
gtaagtgttctcaatatttccttttacttatcatcctcaatacatttatctcattgaaaaggctataaaattctgcattggttcacagGAGGATGCAAGTAAAACTCCAGCTTCAGCGCGACACAAACGAGGCTGTAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
upper sequence: GLYMA11G00920.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------gttagaaaataaactcgacttagtttttcccctaagcaattgaaacatcttttat---aggtatta-attattatctttttgtagGATGACCCAAATAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
| | | | | | || | | | | | | || || ||| || | || ||||||| ||||||| | | |||||| || ||||| |||||||||||| | || ||||||||||| ||||||| ||| | |||||||| |||||||| ||||||
gtaagagctctctattccatctttttattccccccccccccccccctctctcactctctctgtcctccattaatctaagggatgacatcgttatcttgc-acagGATGATGCCAGTAAAACCCCGGCTTCTGCACGACACAAACGTGGCTGCAACTGCAAGAAATCAAACTGTATGAAGAAATACTGTGAATGCTATCAG
upper sequence: GLYMA11G00920.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 7
gttagaaaataaactcgacttagtttttcccctaagcaattgaaacatcttttataggtattaattattatctttt--tgtagGATGACCCAAATAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
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gttaggacataattcttgccttgtgtttatacagaaaatctgaactgctagttaccc-tgttaagtgaggttttctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAGMapped 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|14010947|gb|BG725877.1|BG725877EST: CTGAAATTGGG GATGACCCAAATAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAAC
genomic: CTGAAATTGGGgttagaaaat ... ctttttgtagGATGACCCAAATAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcccctaagcaattgaaacatcttttataggtattaattattatctttttgtagGATGACCCAAATAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
tattaat putative branch site (score: 2)
ttatcttttt putative PPT
aaacatcttttatagg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagaaaataaactcgacttagtttttcccctaagcaattgaaacatcttttataggtattaattattatctttttgtagGATGACCCAAATAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA