Sequence
atgc intronic sequence ATGC exonic sequencetgtgggtttatgtatattactgcattttttaatttttttttctaaatattcatgatagagacactaatatattcttttctttattagaCGGCCAATGCTGTCCCAGTCCTATGTGTAGCAAGAAATGTTGCATGCAATGTCAGAGGTTGTTTTTTCAAG
Basic information
species | Glycine max |
transcript | GLYMA18G42790.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G42790.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g63820.1 (Oryza sativa), 3'ss of exon 4
tgtgggtttatgtatattactgcattttttaatttttttttctaaatattcatgatagagacactaatatattcttttctttattagaCGGCCAATGCTGTCCCAGTCCTATGTGTAGCAAGAAATGTTGCATGCAATGTCAGAGGTTGTTTTTTCAAG
|| | | ||||| ||| ||| || | ||||||| || || | || || | || | | ||||| ||| |||||||| || || || ||||| |||||||||||||| |||||||| | ||| |||| ||||
-gtatttatttgtattttattgc---ttacactttttttggtcaacaatatctcatt------ctggaccctgtttgcatattttagATGGCAAATGCTGTGCCTGTGCTTTGTGTTGCAAGAAATGTTGCTTGCAATGTTCGTGGTGGTTTCTTCAG-
upper sequence: GLYMA18G42790.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G039650_T02 (Zea mays), 3'ss of exon 4
tgtgggtttatgtatattactgcattttttaatttttttttctaaatattcatgatagagacactaatatattcttttctttattagaCGGCCAATGCTGTCCCAGTCCTATGTGTAGCAAGAAATGTTGCATGCAATGTCAGAGGTTGTTTTTTCAAG
| |||| ||| ||| | | | | ||||| | || | |||| | || || || |||| | | | ||||| |||||||||||| ||||| |||||||| ||||| |||||||| |||||||| | ||| | |||||||
---gtacttat-tattttattactctgt---attttgtgttgaacatatacccattatggaatgatatgtatttctataaattttagATGGCCAATGCTGTTCCAGTTCTATGTGTTGCAAGGAATGTTGCTTGCAATGTTCGTGGTGGGTTTTTCAG-
upper sequence: GLYMA18G42790.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G01270.1 (Arabidopsis thaliana), 3'ss of exon 4
---tgtgg--gtttatgtatattactgcattttttaatttttttttctaaatattcatgatagagacactaatatattcttttc----tttattagaCGGCCAATGCTGTCCCAGTCCTATGTGTAGCAAGAAATGTTGCATGCAATGTCAGAGGTTGTTTTTTCAAG
||||| | | || || | || || | | | | | || ||| ||| | | | | || ||| | | ||||| |||| ||| || || ||| || || |||||||||||||||||||||||||||||||||| ||||||||
gcatgtggttgctcttgcatttagttgtgaattaaattctgtatcacttaattttccaagtgggtatctaaccattttcgtatgcccatttatcagACAGCCCTTGTCGTTCCACATCTCTGCGTAGCAAGAAATGTTGCATGCAATGTCAGAGGTTACTTTTTCAA-
upper sequence: GLYMA18G42790.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g02130.t01 (Vitis vinifera), 3'ss of exon 4
------tgtgggtttatgtatattactgcattttttaatttttttttctaaatattcatgatagagacac---taatatat-tcttttctttattagaCGGCCAATGCTGTCCCAGTCCTATGTGTAGCAAGAAATGTTGCATGCAATGTCAGAGGTTGTTTTTTCAAG
| | | |||| | || || || || || || | ||| || | || | ||| || | | || || | ||||| | ||| |||| ||| ||||||||||||||||||||||||| ||||||||||| | ||||||||||
gtaataaattatgctgtctataagattgataattgaaaattgttacattatttcatcaagactggcactaatgtgatacatatatatttttgaatagACAACAAATCCTGTTCCAATCCTATGTGTAGCAAGAAATGTTGCGTGCAATGTCAGGGCGGGTTTTTTCAA-Mapped 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|9903165|gb|BE612133.1|BE612133EST: GTTGTGCCTGCCTTTACTCCTTATTATGCTCCTCAAGCAGAGA CGGCCAATGCTGTCCCAGTCCTATGTGTAGCAAGAAATGTTGCATGCAATG
genomic: GTTGTGCCTGCCTTTACTCCTTATTATGCTCCTCAAGCAGAGGtgtgggttta ... ctttattagaCGGCCAATGCTGTCCCAGTCCTATGTGTAGCAAGAAATGTTGCATGCAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttttctaaatattcatgatagagacactaatatattcttttctttattagaCGGCCAATGCTGTCCCAGTCCTATGTGTAGCAAGAAATGTTGCATGCAATGTCAGAGGTTGTTTTTTCAAG
cactaat putative branch site (score: 2)
tattcttttctttatt CT-rich tract
actaatatattctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgggtttatgtatattactgcattttttaatttttttttctaaatattcatgatagagacactaatatattcttttctttattagaCGGCCAATGCTGTCCCAGTCCTATGTGTAGCAAGAAATGTTGCATGCAATGTCAGAGGTTGTTTTTTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA