Sequence
atgc intronic sequence ATGC exonic sequence...ttaatttgtttgtttttattttgctggctcgttatgttttaagctattgtttgagaatagattgattcatggtttatgatttctttgaacaatgcctcagATATGCCTCAGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCAATGGCTCACTTATTGGGTTCTCTATTCCTTGATCACCCTCTTTGAACTT
Basic information
species | Glycine max |
transcript | GLYMA06G20570.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G20570.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g12220.1 (Oryza sativa), 3'ss of exon 2
-ttaat-ttgtttgtttttattttgctggctcgttatgttttaagctattgtttgagaatagattgattcatggtttatgatttctttgaacaatgcctcagATATGCCTCAGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCAATGGCTCACTTATTGGGTTCTCTATTCCTTGATCACCCTCTTTGAACTT
| | | || ||| || || || | | | || ||| | ||| || | | || || | ||| || |||| || | | |||||||||||| || || ||||| || | || |||||||||||||| ||||||||||||||||| ||||| || || || || ||||| | ||||| |||
gtaagtattattttgttgtaattcaatattttgccat--tttgattgtttgattatttctgttattatatata-tatatatttacttttcgcacttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTT
upper sequence: GLYMA06G20570.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g05990.t01 (Vitis vinifera), 3'ss of exon 2
ttaatttgtttgtttttattttgctggctcgtt-atgttttaagctattgtttgagaatagattgattcatggtttatgatttctttgaacaatgcct----cagATATGCCTCAGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCAATGGCTCACTTATTGGGTTCTCTATTCCTTGATCACCCTCTTTGAACTT
| |||| | ||| | | | | ||| ||||||| || | ||||| | |||| || | ||| || ||| | | | || ||||||||||||| ||||||||||||||| |||||| ||||||||||| |||||||||||||| || |||||| | ||||| ||||||| ||||| || ||
catgtatgttctataatatgtggtttgaatgtttgtgttttag----ttttctgagagaaaattgcttgaaacttt-tgttttggtgggctggtttctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTCMapped 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|17023620|gb|BM094654.1|BM094654EST: GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGG ATATGCCTCAGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCA
genomic: GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGGgtatgttttg ... aatgcctcagATATGCCTCAGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgtttgagaatagattgattcatggtttatgatttctttgaacaatgcctcagATATGCCTCAGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCAATGGCTCACTTATTGGGTTCTCTATTCCTTGATCACCCTCTTTGAACTT
gattgat putative branch site (score: 4)
tttatgatttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaatttgtttgtttttattttgctggctcgttatgttttaagctattgtttgagaatagattgattcatggtttatgatttctttgaacaatgcctcagATATGCCTCAGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCAATGGCTCACTTATTGGGTTCTCTATTCCTTGATCACCCTCTTTGAACTT
- - - tgtttgt
- - - - - - - - - - -tgctggc
- - - - - - - - - - - - - - - - - - - - - gctattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcatgg