Sequence
atgc intronic sequence ATGC exonic sequencegttcttcctctattttttaattttattttcaaattcataccaactcaatcctttttcttgccattttgactttcaacttttccggatttttcagGAGGCTTTAAAGACCATATTAATTATTTTTGCAAAGTTGAACTCAGGTATAAGATATGTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
Basic information
species | Glycine max |
transcript | GLYMA11G36520.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G36520.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g28990.1 (Oryza sativa), 3'ss of exon 5
gttcttcctctatttttt--aattttattttcaaattcataccaactcaatcctttttcttgccattttgactttcaacttttccgg-atttttcagGAGGCTTTAAAGACCATATTAATTATTTTTGCAAAGTTGAACTCAGGTATAAGATATGTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
||| | || | || |||| | || ||| | || | ||| | ||| ||||| |||| || ||||| | |||||||| || ||| | | | ||||| || |||| || || | ||||||||||| ||||||||||||||||| ||||| ||||| || |||||||
gtttcacttcagtgccttggaattccttatttccatttaaacta---caag-----taattgtcatttggacta--aatttttcaaacacatttcagGAATCTCTAAGGCGTGTTCTCATTATCTTCTCAAAATTAAATCCTACCATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTCTTTTTTATGTGT
upper sequence: GLYMA11G36520.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g30880.1 (Oryza sativa), 3'ss of exon 5
gttcttcctctattttttaattttattttcaaattcataccaactcaatcctttttcttgccattttgactttcaacttttccggatttttcagGAGGCTTTAAAGACCATATTAATTATTTTTGCAAAGTTGAACTCAGGTATAAGATATGTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
| | | |||| | | || | || | ||| | || | | || | | | | | | | | | | | |||||||| | ||||| ||| | | || |||||||| || || | |||||||||||||| ||||| ||||||||||| ||||| || |||| |||||| |
-gtaagcatttattatctgatatgatgcc--agttctttttgtcttt-tgtaatgtccagttaggctaaatgtgatatatgtttg--tcttcagGAGTCGCTAAAGCGTATACTTACCATATTTGCAAAATTAAATCCGGGTATAAGATATGTACAAGGAATGAATGAAGTTTTGGCACCACTCTACTATGTTT
upper sequence: GLYMA11G36520.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g68010.3 (Oryza sativa), 3'ss of exon 5
gttcttcctctattttttaattttattttcaaattcataccaactcaatcctttttcttgccattttgactttcaacttttccggatttttcagGAGGCTTTAAAGACCATATTAATTATTTTTGCAAAGTTGAACTCAGGTATAAGATATGTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
| || | | | || || || | || | | || | | | | | | ||| || ||||| || | || | ||| | ||||| ||||||||| |||| | || ||| | ||||| ||||||||||||||| | ||||| |||||||||| |||||
---------------gtgaactccactatctaagtctaaacag---agttctgctcagaaacctgactgatcataggtcatcc----ttaccagGAATCTCTGAAAAATATACTGATTATCTTTGCAAAGCTGAATGCCGGAATACGTTATGTACAAGGGATGAATGAAATTTTGGCACCTCTCTTCTTTGTGT
upper sequence: GLYMA11G36520.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G122935_T01 (Zea mays), 3'ss of exon 5
gttcttcctctattttttaattttattttcaaattcataccaactcaatcctttttcttgccattttgactttcaacttttccggatttttcagGAGGCTTTAAAGACCATATTAATTATTTTTGCAAAGTTGAACTCAGGTATAAGATATGTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
||| ||| | || | | | | | ||| | || || | ||| | |||||| || || | | |||||| | || | || || |||||||| ||| |||| |||||| | ||||||||||||| ||||||||||||||||| ||||| ||| | || ||||| |
-------------gtttgtattcagtgtttacagt-gttcgtactgataccaattg--taccaatatgacttgattattctctgaccctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTAT
upper sequence: GLYMA11G36520.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G068392_T02 (Zea mays), 3'ss of exon 5
gttcttcctctattttttaattttattttcaaattcataccaactcaatcctttttcttgccattttga-ctttcaacttttccggattttt--cagGAGGCTTTAAAGACCATATTAATTATTTTTGCAAAGTTGAACTCAGGTATAAGATATGTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
||| | | || | | ||| || | | | | || | ||| |||| | ||||| ||| | ||||| |||| || | || | | || ||||| ||| |||| | || ||||||||||| ||||||||||||||||| ||||| || ||||||| ||| |
----------------gtaaatctccacgcactctgagttcaaa-cagtgttgtcagatccctgtctgatcttttacctttttattattctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT
upper sequence: GLYMA11G36520.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G022308_T02 (Zea mays), 3'ss of exon 6
gttcttcctctattttttaattttattttcaaattcataccaactcaatcctttttcttgccattttgactttcaacttttccggatttttcagGAGGCTTTAAAGACCATATTAATTATTTTTGCAAAGTTGAACTCAGGTATAAGATATGTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
| | | || | | | | || | ||| | || | ||| | | | | || | ||| ||||| | ||||| ||| | | || |||||||| ||||| | |||||||||||||| ||||| |||||||| || ||||| ||||||| ||||| |
---gtaggtgtgttccctgacatgggatcactttttttttgttgtcagtaacattgttcagtttttctaatgcaatatgttttg---tttctagGAGTCACTAAAGCGTATACTTACAATATTTGCAAAATTGAATCCGGGTATAAGATATGTACAAGGAATGAATGAGGTTTTGGCACCTCTCTATTATGTTT
upper sequence: GLYMA11G36520.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G13730.2 (Arabidopsis thaliana), 3'ss of exon 5
----------gttcttcctctattttttaatttt----attttcaaattcataccaactcaatcctttttcttgccattttgactttcaacttttccggatttttcagGAGGCTTTAAAGACCATATTAATTATTTTTGCAAAGTTGAACTCAGGTATAAGATATGTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
| | || || || ||| | || || | ||| | | || ||||||||| | |||| | || |||| | | | |||| ||||| |||| ||| || | |||||| ||||||||||| | || || |||||||| |||||||||||||| ||||||| ||| | ||||| | |
gttgggtgttggttttgctatagtttaaagcctttgggatgattaaaacatcagtatactgatagtttttcttgtcttttta---tacatgttttgca---tgtctagGATGCTTTGAAGAACATTTTGACTATTTTCGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCT
upper sequence: GLYMA11G36520.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 5
gttcttcctctattttttaattttattttcaaattcataccaactcaatcctttttcttgccattttgactt-tcaacttttccggatttttcagGAGGCTTTAAAGACCATATTAATTATTTTTGCAAAGTTGAACTCAGGTATAAGATATGTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
| | || || | ||| ||| || | |||||| | | || | | | |||||||| ||||| | || |||||| ||| | |||||||||||||| | |||||||||||||| ||||||||||||||| | ||||| ||||| |||||||| |
---------------gtatgtgttgttacttgaggcatga-gacttgatacaaacatcacccatttgaccaaattaaatggatcctgtatttcagGATGCTTTGAGGAACATATTGATTGTGTTTGCAAAGTTGAATCCGGGTATAAGATATGTGCAAGGGATGAATGAAATTTTGGCGCCTCTATTCTATGTATMapped 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|208127508|gb|GD921698.1|GD921698EST: CAGATATAGACTTCTTCTCTGGTGATTCTCATTTTGCAAAATCTAATCAG GAGGCTTTAAAGACCATATTAATTATTTTTGCAAAGTTGAACTCAGGTATA
genomic: CAGATATAGACTTCTTCTCTGGTGATTCTCATTTTGCAAAATCTAATCAGgttcttcctc ... gatttttcagGAGGCTTTAAAGACCATATTAATTATTTTTGCAAAGTTGAACTCAGGTATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaactcaatcctttttcttgccattttgactttcaacttttccggatttttcagGAGGCTTTAAAGACCATATTAATTATTTTTGCAAAGTTGAACTCAGGTATAAGATATGTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
ttttgac putative branch site (score: 3)
tttttc putative PPT
tttttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcttcctctattttttaattttattttcaaattcataccaactcaatcctttttcttgccattttgactttcaacttttccggatttttcagGAGGCTTTAAAGACCATATTAATTATTTTTGCAAAGTTGAACTCAGGTATAAGATATGTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC