Sequence
atgc intronic sequence ATGC exonic sequencegtatgcctctttttccttaaaatatagttgatcctcatctagtgtcaatgtatttagtattttagttatgtacaccctgcaagaggatttcagttaatgttaacattaaaattgacattttaactattaagtatatgacttcatattgcagATATGAAGATGCCTTCAATAGATTTGTGGATGACATCAATAGTTTAGCTACTTATCACTGGTGGGAAGGGTCTATTTACAGTATCCTTTGCATCATTGCA
Basic information
species | Glycine max |
transcript | GLYMA08G03550.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G03550.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G412234_T01 (Zea mays), 3'ss of exon 5
gtatgcctctttttccttaaaatatagttgatcct---------catctagtgtcaatgtatttagtattttagttatgtacacc-----ctgcaagaggatttcagttaatgttaacattaaaattgacatttta---actattaagtata----------tgacttcatattgc---------------agATATGAAGATGCCTTCAATAGATTTGTGGATGACATCAATAGTTTAGCTACTTATCACTGGTGGGAAGGGTCTATTTACAGTATCCTTTGCATCATTGCA
||||| | || | | ||| | | ||| || || | | ||| | | | || ||| || | || || | ||| ||| | | | |||| |||| | | | ||||| | ||| || | || |||| |||||||||||||| || ||||||||||| ||||| || || | | || ||||||| ||||||||||| ||||||||||||||||| || || ||||
gtatgtgtgcttcttcacaaatcacaagtgaatctagatatattcaattggatccaacctttgtggtccttttcttgtaccacccttaagctccgagactcttttgagccaactaaccatttaaatctgcctgtagggtactatcagaaatacttcaaatggtgttctaattttgctttctcttcgttttcagATATGAAGATGCATTTAATAGATTTGTCGATGAGATAAACACCCTTGCAGCTTATCAATGGTGGGAAGGATCTATTTACAGTATCCTCTGTATACTTGCC
upper sequence: GLYMA08G03550.1 (Glycine max), 3'ss of exon 17
lower sequence: PP1S164_9V6.1 (Physcomitrella patens), 3'ss of exon 15
gtatgcctctttttccttaaaatatagttgatcctcatctagtgtcaatgtatttagtattttagttatgtacaccctgcaagaggatttcagttaatgttaacattaaaattgacattttaactattaagtatatgacttcatattgcagATATGAAGATGCCTTCAATAGATTTGTGGATGACATCAATAGTTTAGCTACTTATCACTGGTGGGAAGGGTCTATTTACAGTATCCTTTGCATCATTGCA
|| | | ||| | ||| | || | | | | || || | | || | || | | | | || || | | || || |||||||||| ||||| || || || |||||||| ||| ||||||| ||||| | ||||| |||||||||||||| | | |||||||| || ||||
-----------------------------------------atgctctcctctgctgtaaatcagtaacgtctattttatgaaacttcttttgtaactcgtagttct----ttactagtcttatgatcaaccttct---tttat---gcagATATGAGGATGCTTTTAACAGGTTTGTGGAGGACGTCAATAGCTTAGCAGCATATCAATGGTGGGAAGGGTCCGTGCATAGTATCCTGATAATGCTTGCC
upper sequence: GLYMA08G03550.1 (Glycine max), 3'ss of exon 17
lower sequence: PP1S258_17V6.1 (Physcomitrella patens), 3'ss of exon 11
gtatgcctctttttccttaaaatatagttgatcctcatctagtgtcaatgtatttagtattttagttatgtacaccctgcaagaggatttcagttaatgttaacattaaaattgacattttaactattaagtatatgacttcatattgcagATATGAAGATGCCTTCAATAGATTTGTGGATGACATCAATAGTTTAGCTACTTATCACTGGTGGGAAGGGTCTATTTACAGTATCCTTTGCATCATTGCA-
||| | | | |||| | ||| | || |||| || || | ||||| | | | | ||| || || || ||| | | | || || || | | |||||||||| ||||||||||| || ||||||||||| | ||| | || || | ||||| |||||||| || || | ||||||| || || |||
----------------gtaagtcacacattcccctc-tacagttttgat-tattcag-gttgggatgatgtagat------ataaaaattctcttcctgcaaat-------------tttcatatgtgaaaaatgtggccc---acggcagATATGAGGATGCCTTCAACAGGTTTGTGGATGAGGTGAATGGCTTGGCAGCGTATCAATGGTGGGAGGGCTCAGTGCACAGTATT-TTAACACTATTAGCCMapped 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|193653917|gb|FK598347.1|FK598347EST: GAACCTTGGCATCTACTTCATTGTCCTCCAGAGCAAGTAAAAGATATTGT ATATGAAGATGCCTTCAATAGATTTGTGGATGACATTAATAGTTTAGCTAC
genomic: GAACCTTGGCATCTACCTCATTGTCCTCCAGAGCAAGTAAAAGATATTGTgtatgcctct ... catattgcagATATGAAGATGCCTTCAATAGATTTGTGGATGACATCAATAGTTTAGCTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgttaacattaaaattgacattttaactattaagtatatgacttcatattgcagATATGAAGATGCCTTCAATAGATTTGTGGATGACATCAATAGTTTAGCTACTTATCACTGGTGGGAAGGGTCTATTTACAGTATCCTTTGCATCATTGCA
ttttaac putative branch site (score: 2)
aacattaaaattgaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcctctttttccttaaaatatagttgatcctcatctagtgtcaatgtatttagtattttagttatgtacaccctgcaagaggatttcagttaatgttaacattaaaattgacattttaactattaagtatatgacttcatattgcagATATGAAGATGCCTTCAATAGATTTGTGGATGACATCAATAGTTTAGCTACTTATCACTGGTGGGAAGGGTCTATTTACAGTATCCTTTGCATCATTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG