Sequence
atgc intronic sequence ATGC exonic sequence...gtttattcaaatttcagagttcagtcttcggatctgaagttttgtaattagtgctaatatattacctgcatcctaatcaaaatacttgattttatggtagTGTGGCTCATTTTCTGGAATCACGAGGTATGATAGAAGATGCCCTTGAAGTAGCTACTGACCCTGACTACAGATTTGATCTAGCAATACAGCTTGGAAAA
Basic information
species | Glycine max |
transcript | GLYMA13G43680.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 17
gtttattcaaatttcagagttcagtcttcggatctgaagttttgtaat-tagtgctaatatattacctgcatcctaatcaaaatacttgattttatggtagTGTGGCTCATTTTCTGGAATCACGAGGTATGATAGAAGATGCCCTTGAAGTAGCTACTGACCCTGACTACAGATTTGATCTAGCAATACAGCTTGGAAAA
| || | | |||| | || | | | || | | || ||| | | | | || || || | || | ||||| ||||| ||||||||| ||||||| |||||||| | ||||| || ||||| |||| ||||| ||||||||| ||||| ||||| | ||||||||||||
atatacttagttttctgcactctttttctgtatttcgtccaacttcatgtagagtctgttctcttctagcctca-gttcttgtttctctctcatatggcagTGTTGCTCATTTTTTGGAATCGAGAGGTATGTTGGAAGAGGCTCTTGAGATAGCCACTGATGCTGACTACAAGTTTGACCTAGCTGTGCAGCTTGGAAAA
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 18
gtttattcaaatttcagagttcagtcttcggatctgaagttttgtaattagtgctaatata---ttacctgcatcctaa---tcaaaatacttgatttta--tggtagTGTGGCTCATTTTCTGGAATCACGAGGTATGATAGAAGATGCCCTTGAAGTAGCTACTGACCCTGACTACAGATTTGATCTAGCAATACAGCTTGGAAAA
| | || | | || ||||||| | || |||| || || || || || | | | | || |||| | | |||||||| ||||| || |||||||| || ||| | || || |||||||| |||| ||||||||| | |||||||||||||| || | ||||||||||
-------------gtgccatcctgtttgtctgttcaaaattttgtagtggttgttaatttaaacttttatgtgccccaatgtttatatgatttacttttggcttgcagTGTGGCACATTTCCTTGAATCACGTGGCATGTTGGAGGAAGCCCTTGATATAGCCACTGACCCTAATTACAGATTTGATCTGGCTGTGCAGCTTGGAAGC
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G448913_T01 (Zea mays), 3'ss of exon 6
gtttattcaaatttcagagttcagtcttcggatctgaagttttgtaat-tagtgctaatatattacctgcatcctaatcaaaatacttgattttatggtagTGTGGCTCATTTTCTGGAATCACGAGGTATGATAGAAGATGCCCTTGAAGTAGCTACTGACCCTGACTACAGATTTGATCTAGCAATACAGCTTGGAAAA
| || | | ||| | || | | | || | | || ||| | | | | ||| | || | || | ||||| ||||| ||||||||| ||||||| |||||||| | ||||| || ||||| |||| ||||| ||||||||| ||||| ||||| | ||||||||||||
atatacttagttttttgcactctttttctgtatttcgtccaacttcatgtagagtctgt-tctcttctggcctcagttcttgtttctctctcatatggcagTGTTGCTCATTTTTTGGAATCGAGAGGTATGTTGGAAGAGGCTCTTGAGATAGCCACTGATGCTGACTACAAGTTTGACCTAGCTGTGCAGCTTGGAAAA
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 17
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 21
-------------------------------------------------gtt--tattcaaatttcagagttcagtcttcggatctgaa-gttttgt--aattagtgctaatata-ttacctgcatcctaa--tcaaaatacttgattttatggtagTGTGGCTCATTTTCTGGAATCACGAGGTATGATAGAAGATGCCCTTGAAGTAGCTACTGACCCTGACTACAGATTTGATCTAGCAATACAGCTTGGAAAA
||| || || | || || ||| || | | ||||| |||| || || || ||| || | ||||||| || || || || ||||| || ||| |||| ||||| || |||| ||||||||| || |||||||| ||||| ||||||||||||||||| | || |||||||| || | |
gtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcagCGTGGCACACTTTTTGGAGTCACGTGGCATGACAGAAGATGCTCTAGAAGTAGCAACTGATCCTGACTACAGATTTGAGTTGGCCATACAGCTCGGTAGA
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 17
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 17
-gtttattcaaatttcagagttcagt----cttcggatctgaagttttgtaattagtgctaatatattacctgcatcctaatcaaaatacttgattttatggtagTGTGGCTCATTTTCTGGAATCACGAGGTATGATAGAAGATGCCCTTGAAGTAGCTACTGACCCTGACTACAGATTTGATCTAGCAATACAGCTTGGAAAA
| || | | | | ||| | | | | || | || || ||| | | | | || || | | | || || |||||| |||||||| |||| ||||| || ||||| |||||||| || ||| | || || || ||||||||||||||||| | || ||||| || || | |
gatctact--gactctattgtttaacatagttgcacacctatcaatgggtgtttcgtg--gaca-actctctttatttattttcggacaattttcgacttgttagTGTTGCTCATTTCTTGGAGTCACGGGGAATGATTGAAGATGCTCTGGAAATTGCAACAGATCCTGACTACAGATTTGAGTTGGCCATACAACTGGGTAGA
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 17
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 17
---gtttattcaaatttcagagttcagtcttcggatctgaagt--tttgtaattagtgctaatatattacctgcatcctaatcaaaatacttgattttatggtagTGTGGCTCATTTTCTGGAATCACGAGGTATGATAGAAGATGCCCTTGAAGTAGCTACTGACCCTGACTACAGATTTGATCTAGCAATACAGCTTGGAAAA
||| || || | | |||| | | || | ||| | |||| || | || || ||| | || || ||| | | | || ||||||||||| ||| ||||| | ||||||||| | || ||||| || ||||| || || || |||||||| |||||||||||||| |||||||| || | |
tgaccgcattttttttcca---cttattcttgttgtttcaattcctttttccatagttctgaaat-ttgactgagatgtgatgaagatatattttact-tgctagTGTGGCTCGTTTCTTGGAAGCTCGAGGTATGCTGGAGGATGCACTGGAAGTTGCCACAGATCCTGACTATAGATTTGATCTAGCTATACAGCTAGGCAGA
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 17
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 17
gtttattcaaatttcagagtt-cagtcttcggatctgaagttttgtaattagtg--ctaatatattacctgcatcctaatcaaaatacttgattttatgg-tagTGTGGCTCATTTTCTGGAATCACGAGGTATGATAGAAGATGCCCTTGAAGTAGCTACTGACCCTGACTACAGATTTGATCTAGCAATACAGCTTGGAAAA
| || ||| | | | | | | | | | || || | || || || | ||||| ||||| | || | ||| || || | ||||||||||| ||| |||||||||| ||||||||||| |||||||| |||||||||||||||||||| ||| ||||||| |||||||| |||||||| | |
----tctgaacttttatacccgctgaaaatgaaacaaagatgaattattttgcagtcttttaagtttcttgcatgctaataagaaaagttgtttgaattgctagTGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGTAGCTACTGACCCTGATTACCGATTTGAGCTAGCAATGCAGCTTGGCAGAMapped 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|298199623|gb|HO043500.1|HO043500EST: GAAAGGGCCAATGAAATTCTACCATCAATCCCCAAAGAGCATCATAACAG TGTGGCTCATTTTCTGGAATCACGAGGTATGATAGAAGATGCCCTTGAAGT
genomic: GAAAGGGCCAATGAAATTCTACCATCAATCCCCAAAGAGCATCATAACAGgtaggactta ... tttatggtagTGTGGCTCATTTTCTGGAATCACGAGGTATGATAGAAGATGCCCTTGAAGT
EST:
gi|151398221|gb|EV268099.1|EV268099EST: GAAAGGGCCAATGAAATTCTACCATCAATCCCCAAAGAGCATCATAACAG TGTGGCTCATTTTCTGGAATCACGAGGTATGATAGAAGATGCCCTTGAAGT
genomic: GAAAGGGCCAATGAAATTCTACCATCAATCCCCAAAGAGCATCATAACAGgtaggactta ... tttatggtagTGTGGCTCATTTTCTGGAATCACGAGGTATGATAGAAGATGCCCTTGAAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattagtgctaatatattacctgcatcctaatcaaaatacttgattttatggtagTGTGGCTCATTTTCTGGAATCACGAGGTATGATAGAAGATGCCCTTGAAGTAGCTACTGACCCTGACTACAGATTTGATCTAGCAATACAGCTTGGAAAA
taatcaaaatacttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttattcaaatttcagagttcagtcttcggatctgaagttttgtaattagtgctaatatattacctgcatcctaatcaaaatacttgattttatggtagTGTGGCTCATTTTCTGGAATCACGAGGTATGATAGAAGATGCCCTTGAAGTAGCTACTGACCCTGACTACAGATTTGATCTAGCAATACAGCTTGGAAAA
- - - - - - - - - - - - - - - - - - - - - - - -ttagtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acctgca