Sequence
atgc intronic sequence ATGC exonic sequence...agctttaaaataataatctgccccttagttttaattatttccacttttttttttaagcatgttgactggtgtctgacttgtgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT
Basic information
species | Glycine max |
transcript | GLYMA08G22140.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 11
-agctttaaaataataatctgccccttagttttaattatttccacttttttttttaagcatgttgactggtgtctgacttgtgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT
| ||| |||| || | | ||| | ||| | |||||| | | | | | | | | | | | || | || | ||||||| ||||||||||||||||||| || || |||||||| ||||||||||| ||||| || || ||||| || ||||||||||||||||||||||| || |
cggttttgaaattgtacttgtcgggttaaata-aatgtgatgaacttttctacgttctggtttatgtttgcatgttattaataatagtgtattcatttcagAGTTTAAGGCACAATCCAAATGGAAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACCGCATTGGCATGGAGAAATAGATCATTCGGGT
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
---agctttaaaataataatctgccccttagttttaattatttccacttttttttttaagcatgttgactggtgtctgacttgtgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT
|| || ||| | | | | ||| | | | | || | | ||||| | | | || | | || || ||| |||||| ||||||||||||| |||||||| || |||||||| ||||||||||| ||||| || || |||||||| || |||||||||||||||||||| || |
gattctgttgttgtagtaaaattaaattaatctcaaatctagtatagtgtaattatagtgtatgttagtaattatagtaattatagtgta--ttcatt-tcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 11
agctttaaaataataatctgccccttagttttaattatttccactt-ttttttttaagcatgttgactggtgtctgacttg-tgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT
| | | | | | | || || | | || | | | | || ||| || ||| | ||| ||| | || | | | || | ||||||| ||||||||||||| |||||||| || || ||||| ||||||||||| ||||| || |||||||| || || ||||||||||| ||||||||||| |
atcatgattttttttaaaacttgttttgtgtcatgcataccagcatatcttatttgtgctagttta--ggttaatgatatactggtgtgatatttgtttcagAGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGAGAATACATAATATACACAGCCTTAGCATGGAGAAACAGATCATTTGGGT
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 11
---agctttaaaataataatctgccccttagttt-taattatttccacttttttttttaagcatgttgactggtgtctgacttgtgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT
| ||| || || | | ||| ||| | | || | | |||||| | || ||| || | | | || | | | || | |||||| |||| |||||||| |||||||| || |||||||| ||||||||||| ||||| || |||||||| || || ||||||||||||||||||||||| |
gtttgaattatcatgattttttaaaacttgttttgtggtcatgtatatcttttttgt---gctggtttac-attattaatatactggtgtgatatttgtttcagAGCTTAAGACACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATATACACAGCATTAGCATGGAGAAATAGATCATTTGGGT
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 12
-agcttta-aaataataatctgccccttagttttaattatttccacttttttttttaagcatgttgactggtgtctgacttgtgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT
|||| | || || || |||||| || || || | || || || | | ||| | ||| || || ||| |||||| || |||||||||||||||||||||| |||| ||| ||||||||||| || || ||||| ||||| || | ||||||||||||||||| ||||| |
tttttttatggaaggaaaaaggcaccggttttttaaaagttagttctaacttatgctaggatatttaaaaaacagtaactaatccttt-ctgttcttc-cagAGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGAGAGTACATTATCTACACAGCGCTAGCATGGAGAAATAGATCCTTTGGGT
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
agctttaaaataataatctgccccttagttttaattatt---tccactttttttttta-agcatgttgactggtgtctgacttgtgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT
| | | | | || | | || | |||||| | | | ||| | | ||| | | |||| || | ||||| | | ||| || || ||||| ||||||||||||| ||||||||||| || || || || || ||||| |||| ||||| |||||||||||||| |
ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatctgat-tgtgagtaatcattttggttggt---cagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 10
----------------------------------------------agctttaaaataataatctgccccttagttttaattatttccacttttttttttaag------catgttgactggtgtctgac----ttgtgat---ttacttttattc--tcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT
| || | ||| | || ||| | | | ||| | ||| || ||| ||| ||| ||| || | | ||||||| ||| |||| | |||||| | | ||| ||||| ||||| ||||||||||||| ||||||||||| || || || || || ||||| |||| ||||| ||||| |||||||| |
gtacttttggatgctgatgtgttctttgtattttaaaacttgttactattgtaggtttatagtgtggtttttaagtggacatcttttcgttttattatttggtggtgctcattttgtgtggcgtataatctgattgtgattaattatttttggttggtcagAGCTTGAAGCATAATCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGTGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGGTCATTTGGAT
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 11
---agctttaaaataataatctgccccttagttttaattatttccacttttttttttaagcatgttgactggtgtctgacttgtgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT
|| | ||| | || | | || || | | | | | | | | || |||| |||||| | |||| | || | |||||||| | | |||||| || ||||||||||| || || || ||||| || || |||||||| || ||||| |||||||| ||||||||||| ||||||||||
aagtgcctcaaagttatggg-tatcgctaagccgcg-tcttcagaatatatatctgttctcac-ttgatctgtgtctcatatgtgggtactcttgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGAGAATATATAATCTACACGGCTTTGGCTTGGAGAAATAGGTCATTTGGTT
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 15
agctttaaaataataatctgccccttagttttaa-ttattt-ccacttttttttttaagcatgttgactggtgtctgacttgtg-atttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT
|| || || | | | |||| | |||| | |||| | || || | | | ||| | || | | || || || |||||| | | |||||| || ||||| ||||| || || |||||||||||||| || |||||||| |||||||| ||||| ||| ||||||| |||||||| |
---ttactggtattagtaagaaatatgaccttaaatcatttattaattttgtgactacccactgtcatttatgtttctattatttaattttttgctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
agctttaaaataataatctgccccttagttttaattatttccacttttttttttaagcatgttgac-tggtgtctgacttgtgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT
| | |||| ||| | || | || | | ||| | | | || || | | | || || || | | | | | | | |||||||| | | |||||| || ||||||||||| || || || || || ||||| || || || || |||||||||||||| |||||||||||||| ||||| |
taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagct-attctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 11
agctttaaaataataatctgccccttagttttaattatttccacttttttttttaagcatgttgac--tggtgtctgacttgtgatttacttttatt--ctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT
|| |||| || | || | |||| | || | ||| || ||| ||||| || | | ||| ||| | ||| |||| | |||||| |||| || || |||||||||||||| |||||||||||||||||||| || || |||||||| || |||||||||||||| ||||| || |||||||
-gcattaagctagga---tgaatgattgtttccaccatattttaatttattgttatttatgtttacatttatttcttccttttttttttttttttgtgtttcagAGCCTAAAACATAACCCAAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGTGAGTACATTATATATACAGCTTTGGCATGGAGGAATAGGTCTTTTGGTT
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
agctttaaaataataatctgccccttagttttaattatttccacttttttttttaa-gcatgttgactggtgtctgacttgtgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT
| ||| ||| | | | | | | | || ||||||| || ||| || | || || | | ||| ||||| | ||||||| | | ||||||| | ||||| |||| |||||||||||||| ||||||||||| || |||||||| |||||||||||||||||||||||||||| |
actttttctctaagaggcagtgcatagaatatgtgcgggctcagtttttttgttgtcacattatggttaatgacttttgtttt-tttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S243_63V6.1 (Physcomitrella patens), 3'ss of exon 11
-----agctttaaaataataatctgccccttagttttaattatttccactttttttt-ttaagcatgttgactg-gtgtctgacttgtgatttacttt-tattct---cagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT
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gtgaccgattgctcgtctaaatttctttttgaaatttcatcttcgaaagatatgtttgctcaaaatatctatcaagtgaacgcttatcggttggctttgtgtgccttgcagAGCCTGAAACATAATCCGAATGGCAGGTTTGTGGTAGTTTGTGGTGATGGTGAGTATATTATCTACACAGCTCTTGCTTGGAGGAATCGATCATTTGGTTMapped 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|193660238|gb|FK603064.1|FK603064EST: GGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCTCAA AGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGG
genomic: GGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCTCAAgtgagtgaac ... ttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGG
EST:
gi|193334327|gb|FK297571.1|FK297571EST: GGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCTCAA AGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGG
genomic: GGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCTCAAgtgagtgaac ... ttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttttttaagcatgttgactggtgtctgacttgtgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT
gtctgac putative branch site (score: 3)
tttacttttattctc putative PPT
tgatttacttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agctttaaaataataatctgccccttagttttaattatttccacttttttttttaagcatgttgactggtgtctgacttgtgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - aaaataa
- - - - - - - - -ctgcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acttgtg