Sequence
atgc intronic sequence ATGC exonic sequence...taaatgtgtacagctgcacttggatagttttgttggtggattcttctaatttatctatgtctgaatctatgtgtttatttttgtgatgttccctggttagACTATAATTTGCTGGAGGAGGTGAAGAGGGTGGCTGAATCTGCTCAAAGAATGAGAAATAAATTGGGCATTTATGCCTATTTTAAGTTACCTCGTTACCT
Basic information
species | Glycine max |
transcript | GLYMA16G32840.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G32840.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0088g00200.t01 (Vitis vinifera), 3'ss of exon 1
-taaatgtgtacagctgcacttggatagttttgttggtggattcttctaatttatctatgtctgaatctatgtgtttatttttgtgatgttccctg-gttagACTATAATTTGCTGGAGGAGGTGAAGAGGGTGGCTGAATCTGCTCAAAGAATGAGAAATAAATTGGGCATTTATGCCTATTTTAAGTTACCTCGTTACCT
| | | | | ||| | ||||||| || |||| |||| || | | | | | || | | | || | | |||| || |||||||| ||||| |||||||| || || |||||||||||||||| |||| |||| || || ||| | | ||||||| || | ||
atgggtaaattatgattttgttgaggaagtttgttg-tgttgtctttggatttcact-tacccaattttcagtttaaaagaaaaaggaattttttttggtagATTACAATTTGCTCGAGGAAGTGAAGAGTGTTGCAGAATCTGCTCAAAGAAGGAGAGTTAAACTGTGCGGGTATTCTCAGCTTAAGTTTCCATACCATCT
upper sequence: GLYMA16G32840.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0048g00080.t01 (Vitis vinifera), 3'ss of exon 2
taaatgtgtacagctgcacttggatagttttgttggtggattcttctaatttatctat-gtctgaatctatgtgtttatttttgtgatgttccctggt--tagACTATAATTTGCTGGAGGAGGTGAAGAGGGTGGCTGAATCTGCTCAAAGAATGAGAAATAAATTGGGCATTTATGCCTATTTTAAGTTACCTCGTTACCT
| | || | | | | ||| | ||||| | | | | | || ||| | | | || ||| | |||| ||| | | |||| ||||||||||| ||||| ||||||||||| || |||||||| || |||| ||| ||| ||| || || | |||||||| | || | |
tttttaattatgggtaaatt---ataatattgttaaggaagtttgttgtgttgtcttcagatttcacttaccctttttgcagtttgattttcttttttggtagATTATAATTTGCTCGAGGAAGTGAAGAGGGTTGCAGAATCTGCGCAGAGAACAAGAGTTAATTTGTGCGGGCATTCTCATTTTAAGATTCCATCCCATCC
upper sequence: GLYMA16G32840.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0048g00030.t01 (Vitis vinifera), 3'ss of exon 2
-----taaatgtgtacagctgcacttggatagttttgttggtggattcttctaatttatctatgtctgaatctatgtgtttatttttgtgatgttccctggttagACTATAATTTGCTGGAGGAGGTGAAGAGGGTGGCTGAATCTGCTCAAAGAATGAGAAATAAATTGGGCATTTATGCCTATTTTAAGTTACCTCGTTACCT
| || | | | | ||||||| | | || || | || | | | ||||||| | | || | |||| ||| ||||||||| | ||||| ||||||||||| || ||||||||||| |||| |||| ||| ||| ||| | |||||||| | || | ||
aattatgggtgaattataatattgtcaaggaagtttgttgtgttgtcttcatatttcacttaccctt---tttgcagttttatttattt-atttattttggt-agATTATAATTTGTTCGAGGAAGTGAAGAGGGTCGCAGAATCTGCTCAGAGAACAAGAATTAATTTGTTTGGGTATTCTCATTTTAAGATTCCATCCCATCTMapped 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|7587909|gb|AW703715.1|AW703715EST: GACTCAGTTTCTTCCTCTTTCGAAGTTTGATGACAGTGTCCTGTTATCTG ACTATAATTTGCTGGAGGAGGTGAAGAGGGTGGCTGAATCTGCTCAAAGAA
genomic: GACTCAGTTTCTTCCTCTTTCGAAGTTTGATGACAGTGTCCTGTTATCTGgtactttgct ... ccctggttagACTATAATTTGCTGGAGGAGGTGAAGAGGGTGGCTGAATCTGCTCAAAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaatttatctatgtctgaatctatgtgtttatttttgtgatgttccctggttagACTATAATTTGCTGGAGGAGGTGAAGAGGGTGGCTGAATCTGCTCAAAGAATGAGAAATAAATTGGGCATTTATGCCTATTTTAAGTTACCTCGTTACCT
ttctaat putative branch site (score: 2)
tgttccct putative PPT
tatgtgtttattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaatgtgtacagctgcacttggatagttttgttggtggattcttctaatttatctatgtctgaatctatgtgtttatttttgtgatgttccctggttagACTATAATTTGCTGGAGGAGGTGAAGAGGGTGGCTGAATCTGCTCAAAGAATGAGAAATAAATTGGGCATTTATGCCTATTTTAAGTTACCTCGTTACCT
- - tgtgtac
- - - - - - - tgcactt
- - - - - - - - - - - - - - - - -tggtgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtt