Sequence
atgc intronic sequence ATGC exonic sequence...aatccatgttgttacatggtgaaacattttataccttgtcatgtcaacctattcatatttatcatgtgtgtgtcctcactgaattcaacaatctttccagATCAAAGACTGCAGAACACGTTACAACGGTGATGCTGATCATCATCAACGACGTAAAAAGTTTACATTTCCTGCTCGCCTTATATGTGGAGATTGTTATG
Basic information
species | Glycine max |
transcript | GLYMA08G22390.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G22390.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G20650.2 (Arabidopsis thaliana), 3'ss of exon 4
---aatccatgttgttacatggtgaaacattttataccttgtcatgt-caacctattcatatttatcatgtgtgtgtcctcactgaattcaacaatctttccagATCAAAGACTGCAGAACACGTTACAACGGTGATGCTGATCATCATCAACGACGTAAAAAGTTTACATTTCCTGCTCGCCTTATATGTGGAGATTGTTATG
| | | | | | ||| | | | || ||| ||| | ||| ||| | | ||| || || | | || || ||||| |||| || | || ||||| ||||||||||| || ||||||||||| ||||||||||| | ||||| |||| | ||||||| ||||||| ||
gtaagtttac-tggctgaatgatagctgtatctttattttg-catatatgttttatctctatacctgagaagtgcttctatgttgtacttaataa------cagATTGAAGATTGTCGCACGCGTTATAACGGTGATGCAGACCATCATCAACGGCGTAAAAAGTTCAGTTTTCCGTCTCGATTATTATGTGGGGATTGTTTTG
upper sequence: GLYMA08G22390.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0023g02860.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------aatccatgttgttacatggtgaaacattttataccttgtcatgtcaacctattcatatttatcatgtgtgtgtcctcactgaattcaacaatctttccagATCAAAGACTGCAGAACACGTTACAACGGTGATGCTGATCATCATCAACGACGTAAAAAGTTTACATTTCCTGCTCGCCTTATATGTGGAGATTGTTATG--
| | || | || | | | || | | || ||| | | | || | | || | ||| ||| | | | | ||| ||||||| | ||||| || || ||||| || ||||||||| | || |||||||| |||||||| |||||||||||||||||||||| || ||
gtgtcctcattcagctttatgctctccgaggggatgctgttcttgattttgctcgtggcaagggtggtgatctaatcaaataggacaaggcaaagattggatac-tatgttggcaccaatattgctgaaggctt--gatagaagACTGTTGTACACGCTATAATGGTGACATAGACCATCATCAAAGGCGCAAAAAGTTCACATTTCCGGCTCGCCTTATATGTGGAGATTATTTTGAG
upper sequence: GLYMA08G22390.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0014g04740.t01 (Vitis vinifera), 3'ss of exon 4
aatccatgttgttacatggtgaaacattttataccttgtcatgtcaacctattcatatttatcatgtgtgtgtcc-tcactgaattcaacaatctt-tccagATCAAAGACTGCAGAACACGTTACAACGGTGATGCTGATCATCATCAACGACGTAAAAAGTTTACATTTCCTGCTCGCCTTATATGTGGAGATTGTTATG
| |||| | || |||| |||| | ||||| | | | | | || || | ||| || || ||| | | ||||| |||||||| | ||||| || || ||||| || || ||||||||||| || |||||||| |||||||| ||||||||||||||||||||||||| ||
-aggcatggcaaga-attttgaatttttttctcaattgtctctgctgttgcatgtttgctgttataaacttgcctatcattgtgtttggcaactatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGGCGCAAAAAGTTCACATTTCCGGCTCGCCTTATATGTGGAGATTGTTTTGMapped 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|298178509|gb|HO024244.1|HO024244EST: ACAAGGCCAAAATTGGATATTATGTTGGTATTGACATTGCTGAAGGCTCA ATCAAAGACTGCAGAACACGTTACAACGGTGATGCTGATCATCATCAACGA
genomic: ACAAGGCCAAAATTGGATATTATGTTGGTATTGACATTGCTGAAGGCTCAgtaagtatta ... atctttccagATCAAAGACTGCAGAACACGTTACAACGGTGATGCTGATCATCATCAACGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacctattcatatttatcatgtgtgtgtcctcactgaattcaacaatctttccagATCAAAGACTGCAGAACACGTTACAACGGTGATGCTGATCATCATCAACGACGTAAAAAGTTTACATTTCCTGCTCGCCTTATATGTGGAGATTGTTATG
tcctcac putative branch site (score: 2)
tctttcc putative PPT
attcatatttatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatccatgttgttacatggtgaaacattttataccttgtcatgtcaacctattcatatttatcatgtgtgtgtcctcactgaattcaacaatctttccagATCAAAGACTGCAGAACACGTTACAACGGTGATGCTGATCATCATCAACGACGTAAAAAGTTTACATTTCCTGCTCGCCTTATATGTGGAGATTGTTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- -ccatgtt
- - - - - - - catggtg
- - - - - - - - - - - - - - - -taccttg
- - - - - - - - - - - - - - - - - - - tcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - ctattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtgtg