Sequence
atgc intronic sequence ATGC exonic sequenceAGTTCTCAGTCGTGATGTATACAGACTTGGGCAGCTTTTTGATTTCTTCCGGATGCTGTCTTTTTATTTTACAACAGTTGGGTACTACTTTTGTACCATGgtatgccaattatgcgtcatttatttttgtttattgaatgaataagtatgttagtgcacctagactgcaacacaacacaacagacaatgggaccctttta...
Basic information
species | Glycine max |
transcript | GLYMA20G38860.1 |
intron # | 43 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G38860.1 (Glycine max), 5'ss of exon 43
lower sequence: LOC_Os03g02756.1 (Oryza sativa), 5'ss of exon 7
AGTTCTCAGTCGTGATGTATACAGACTTGGGCAGCTTTTTGATTTCTTCCGGATGCTGTCTTTTTATTTTACAACAGTTGGGTACTACTTTTGTACCATGgtatgccaattatgcgtcatttatttttgtttattgaatgaataagtatgttagtgcacctagactgcaacacaacacaacagacaatgggaccctttta----
||| ||||| || ||| ||||||||||||| ||||||||||| || ||| ||||| |||| || ||| | ||||| |||||| |||||| || ||||||||| ||| | | | || || || | | | ||||| |||| | | | | || | ||| | | | || | | |
AGTGCTCAGCCGGGATATATACAGACTTGGACAGCTTTTTGACTTTTTCAGGATGTTGTCCTTCTATGTGACAACTATTGGGTTCTACTTCTGCACCATGgtaattagattttcc-ttgcttgttattccctcattcacgaatag--atgtcactttagaatgtctttagttgaacttt-taaaagtttggctacctccatttt
upper sequence: GLYMA20G38860.1 (Glycine max), 5'ss of exon 43
lower sequence: AT3G07160.1 (Arabidopsis thaliana), 5'ss of exon 40
AGTTCTCAGTCGTGATGTATACAGACTTGGGCAGCTTTTTGATTTCTTCCGGATGCTGTCTTTTTATTTTACAACAGTTGGGTACTACTTTTGTACCATGgtatgccaattatgcgtcatttatttttgtttattgaatgaataagtatgttagtgcacctagactgcaacaca-acacaacagacaatgggaccctttta---
||||| ||||| ||||||||||||||||| ||||| ||||||||||||| ||| |||| || | |||||||| ||||| | ||| | ||||| |||||||| | | || | | | ||| || | | | || | | || || | ||| | | | || |
GGTTCTTAGTCGAGATGTATACAGACTTGGCCAGCTCCTTGATTTCTTCCGTATGATGTCATTCTTCTTTACAACCGTTGGCTTCTATCTATGTACAATGgtatgtggaccctctttcg---aatcacagtgattttatttgcctct-taccattgtattcaagttgatacctgcatccaattcctgaatgtttaccttcatat
upper sequence: GLYMA20G38860.1 (Glycine max), 5'ss of exon 43
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 5'ss of exon 38
AGTTCTCAGTCGTGATGTATACAGACTTGGGCAGCTTTTTGATTTCTTCCGGATGCTGTCTTTTTATTTTACAACAGTTGGGTACTACTTTTGTACCATGgtatgccaattatgcgt--catttatttttgtttattgaatgaataagtatgttagtgcacctagactgcaacacaacacaacagacaatgggaccctttta
|||||||||||| || | ||||||||||||||||| |||||||||||||| ||| |||| || || ||||| || ||||| ||||| || ||||| |||||||| | || ||| | |||| | ||| || | | | | | | | ||| | | | || | | | |||
AGTTCTCAGTCGAGACATTTACAGACTTGGGCAGCTCTTTGATTTCTTCCGAATGATGTCATTCTACTTTACGACTGTTGGATACTATTTCTGTACTATGgtatggaatttctgcatttcattaactttaaattgctca--ggtcctttgggctcaaaaaactaaaagaaatgaaaatatgtggactgtttaggattcattaMapped 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|24205419|gb|BU964672.1|BU964672EST: GGATGCTGTCTTTTTATTTTACAACAGTTGGGTACTACTTTTGTACCATG CTAACAGTGCTGACTGTATATGCCTTTCTATATGGGAAAGCATATTTG
genomic: GGATGCTGTCTTTTTATTTTACAACAGTTGGGTACTACTTTTGTACCATGgtatgccaat ... catcctgcagCTAACAGTGCTGACTGTATATGCCTTTCTATATGGGAAAGCATATTTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGTTCTCAGTCGTGATGTATACAGACTTGGGCAGCTTTTTGATTTCTTCCGGATGCTGTCTTTTTATTTTACAACAGTTGGGTACTACTTTTGTACCATGgtatgccaattatgcgtcatttatttttgtttattgaatgaataagtatgttagtgcacctagactgcaacacaacacaacagacaatgggaccctttta
- - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG