Sequence
atgc intronic sequence ATGC exonic sequencegttagtcttgatatattctatcttagacttgttatttgcatataatttaattttgtaaggttaaattaaacttctatgtagGTACGTAGCTCCTGAATATGCCATGACTGGGCACCTACTTGTTAAAAGTGATGTTTATAGCTATGGTGTTGTCTTGCTGGAACTGCTTACTGGTAGGAAG
Basic information
species | Glycine max |
transcript | GLYMA19G40500.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G40500.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G180065_T01 (Zea mays), 3'ss of exon 6
gttagtcttgatatattctatc--ttagactt--gttatttgcatataatttaattttgtaaggttaaattaaacttcta-------------tgtagGTACGTAGCTCCTGAATATGCCATGACTGGGCACCTACTTGTTAAAAGTGATGTTTATAGCTATGGTGTTGTCTTGCTGGAACTGCTTACTGGTAGGAAG
|| ||| || | | | | |||| | | || | || | | || ||||| | | ||| || | ||| || || ||||| || || || || || |||||||| || ||| | ||||| ||||||||||| ||||||||||| ||||| | || ||||| || ||||| |||| |
-gtaatctgaatgtccttttacatttagccatgggtccatggcccagcaatttattttctgaatttaccttcaccttgtacttctggcctttttgcagGTATGTTGCACCGGAGTACGCCATGACAGGACACTTGCTTGTAAAAAGTGATGTATATAGCTATGGAGTTGTTCTACTTGAACTACTAACTGGGAGGAGG
upper sequence: GLYMA19G40500.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G02010.1 (Arabidopsis thaliana), 3'ss of exon 6
gttagtcttgatatattctatcttagacttgttatttg-catataatttaattttgtaaggttaaatta-aacttctatgtagGTACGTAGCTCCTGAATATGCCATGACTGGGCACCTACTTGTTAAAAGTGATGTTTATAGCTATGGTGTTGTCTTGCTGGAACTGCTTACTGGTAGGAAG
|| ||| | |||| || || ||| | | |||| ||| | || | | | | || || || || ||||||||||| ||||| || |||||||| || || |||||||||||||| || ||||| ||| | || ||| || | |||||||| ||
gtgagt-tgctcatatctctcgacagttttcatatacaaccttaaattctgagttgcctattgaatccgcgatctgttttcagATATGTTGCGCCTGAATATGCAATGACGGGACACCTACTCGTCAAGAGTGATGTTTATAGTTACGGTGTGGTCCTTCTCGAATTGTTAACTGGTAGAAAA
upper sequence: GLYMA19G40500.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0005g01590.t01 (Vitis vinifera), 3'ss of exon 5
gttagtcttgatatattctatcttagacttg--ttatttgcatataatttaattttgtaaggttaaattaaacttctatgtagGTACGTAGCTCCTGAATATGCCATGACTGGGCACCTACTTGTTAAAAGTGATGTTTATAGCTATGGTGTTGTCTTGCTGGAACTGCTTACTGGTAGGAAG
||| ||| | | | | | | || ||| ||| | | || |||||| | | | |||| | | | ||||| ||||| ||||| ||||| |||||||| || ||||| || |||||||||||||| |||||||| |||||| | || || || | || || || | |
gtttgtcatactctctcatcttttgtccttaacttagtattacctagtttaatgtgtagtaatgttactaaattggtttacagGTATGTAGCCCCTGAGTATGCTATGACTGGACATCTACTAGTAAAAAGTGATGTTTACAGCTATGGAGTTGTCCTCCTTGAGTTGTTGACAGGGAGAAGG
upper sequence: GLYMA19G40500.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S478_19V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------------------------------gttagtcttgatatattctatcttagacttgttatttgcatataatttaatt--ttgtaaggttaaattaaacttctat----gtagGTACGTAGCTCCTGAATATGCCATGACTGGGCACCTACTTGTTAAAAGTGATGTTTATAGCTATGGTGTTGTCTTGCTGGAACTGCTTACTGGTAGGAAG
|| | | | || | || | | ||| | | || || | || || || ||| || | |||| || || || || |||||||| ||||||||||| |||||||| || ||||||||||| || |||| ||| || || ||| | || | || | || ||||||
gtaattattacgttcttttccacaagttacttcttgtacgagaatcaattttagacctgatttcttgtcctctaaatcaatttgaatgtattactagaattcaaatgtcttgtttctactcttatgtttactttcttgtctgacagATATGTGGCACCTGAATACGCCATGACTGGACACCTACTGGTGAAAAGTGATGTCTACAGCTTTGGAGTAGTGTTGTTAGAGTTACTCTCAGGCAGGAAG
upper sequence: GLYMA19G40500.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S116_191V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------------------------gttagtcttgatatattctatct---tagacttgttatttgcat-----------------ataatttaattttg---taaggttaaattaaacttctatgtagGTACGTAGCTCCTGAATATGCCATGACTGGGCACCTACTTGTTAAAAGTGATGTTTATAGCTATGGTGTTGTCTTGCTGGAACTGCTTACTGGTAGGAAG
| ||| | || || ||| | | | || | | ||| | ||| | ||| | | | | ||| || | | ||||||||| || || |||||||| |||||||||||||| || || ||||||||||| || || | ||| ||||| || |||| | | | || ||||||
gtaattaataccttccattccaacgactagccctcaaattgctctctagtgatcagttaccagatcttttatttgcacaacttagtgaaatacattgccggagtttaaagagaaaatctgattctactctcatgctaacttttcttgtttgatagGTACGTGGCACCCGAATATGCTATGACTGGGCACCTGCTGGTGAAAAGTGATGTCTACAGTTTTGGGGTTGTAATGTTGGAGTTATTGTCAGGCAGGAAGMapped 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|21888950|gb|BQ742163.1|BQ742163EST: GGAAGATCTAATTATTTGTCTACTCGTGTCATGGGGACATTTGG GTACGTAGCTCCTGAATATGCCATGACTGGGCACCTACTTGTTAAAAGTGA
genomic: GGAAGATCTAATTATTTGTCTACTCGTGTCATGGGGACATTTGGgttagtcttg ... ttctatgtagGTACGTAGCTCCTGAATATGCCATGACTGGGCACCTACTTGTTAAAAGTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttgttatttgcatataatttaattttgtaaggttaaattaaacttctatgtagGTACGTAGCTCCTGAATATGCCATGACTGGGCACCTACTTGTTAAAAGTGATGTTTATAGCTATGGTGTTGTCTTGCTGGAACTGCTTACTGGTAGGAAG
atttaat putative branch site (score: 4)
cttctat putative PPT
ttatttgcatataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtcttgatatattctatcttagacttgttatttgcatataatttaattttgtaaggttaaattaaacttctatgtagGTACGTAGCTCCTGAATATGCCATGACTGGGCACCTACTTGTTAAAAGTGATGTTTATAGCTATGGTGTTGTCTTGCTGGAACTGCTTACTGGTAGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA