Sequence
atgc intronic sequence ATGC exonic sequence...tacatattttaatattgtgtgatttgttcaattgagtgtatggtttaagcatttgaagaacttaacattattttcttactggaattttgtttattttcagGTGGAAAACAATTTGTGCACTCCAAAAAATGGCGAGATTCTGGTTGCTTCTACTCAAGACTTTTTAACATCTTCCTTTCTCATAACCAGGAAAGATACTT
Basic information
species | Glycine max |
transcript | GLYMA11G15530.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G15530.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S26_192V6.1 (Physcomitrella patens), 3'ss of exon 11
----------------------tacatatt-ttaatattgtgtg---atttgttcaattgagtgtatggtttaagcatttgaagaactta--acattattttctt-----actgg-aattttgtttattttcagGTGGAAAACAATTTGTGCACTCCAAAAAATGGCGAGATTCTGGTTGCTTCTACTCAAGACTTTTTAACATCTTCCTTTCTCATAACCAGGAAAGATACTT
|| | || |||| ||| || | | |||| ||| || || || ||||| | | |||| | || || |||| | | |||||| || ||||||| ||||||||||| ||||| || ||||||||||| |||||||||| || || || || || |||||||| | | | || ||||| || ||||
gtacactgctcctttttgacattaagtcttgttaaagctgtctgctgaccttgtcaagaaagtctaca--ttgagggtttgatgcctctcttacatcgtgtttttcatgtactgatagtcttgtttgctt-cagGTGGCCAACAATTTGTGTACTCCTAAGAATGGCGAGATATTGGTTGCTTCAACACAGGATTTCTTGACATCTTCTTACTTGTTCACAAGGAAGGACACTT
upper sequence: GLYMA11G15530.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ13293 (Selaginella moellendorffii), 3'ss of exon 11
tacatattttaatattgtgtgatttgttcaattgagtgtatggtttaagcatttgaagaacttaacattattttcttactg-gaattttgtttattttcagGTGGAAAACAATTTGTGCACTCCAAAAAATGGCGAGATTCTGGTTGCTTCTACTCAAGACTTTTTAACATCTTCCTTTCTCATAACCAGGAAAGATACTT
|||| | || ||| | ||| ||| | ||| | | | |||||||||| ||||||| |||||||| || || |||||||| ||||||||||| ||||||||||| || || || || || ||||| |||||||||| ||||||||
--------------------------------------------gtaagaa--tgctttgctttgctttagattcaaataacgaaagtcgat--ttttcagGTGCAAAACAACTTGTGCACACCCAAGAATGGCGAAATTCTGGTTGCATCTACTCAAGATTTCTTGACGTCGTCATTTCTTATAACCAGGAGAGATACTT
upper sequence: GLYMA11G15530.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ24638 (Selaginella moellendorffii), 3'ss of exon 11
tacatattttaatattgtgtgatttgttcaattgagtgtatggtttaagcatttgaagaacttaacattattttct--tactggaattttgtttattttcagGTGGAAAACAATTTGTGCACTCCAAAAAATGGCGAGATTCTGGTTGCTTCTACTCAAGACTTTTTAACATCTTCCTTTCTCATAACCAGGAAAGATACTT
|||| | || || | ||| ||| || || || || ||||||||||| ||||||| |||||||| || || |||||||| ||||||||||| ||||||||||| || || || || || ||||| |||||||||| ||||||||
--------------------------------------------gtaagaa--tgctttgtttcgctttagattcaaataatgaaa----gtcgattttcagGTGCAAAACAACTTGTGCACACCCAAGAATGGCGAAATTCTGGTTGCATCTACTCAAGATTTCTTGACGTCGTCATTTCTTATAACCAGGAGAGATACTTMapped 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|18040622|gb|BM308916.1|BM308916EST: ACTGAGGAGGCTAGGACAGAGGCTATTTTGTTGATGGGG GTGGAAAACAATTTGTGCACTCCAAAAAATGGCGAGATTCTGGTTGCTTCT
genomic: ACTGAGGAGGCTAGGACAGAGGCTATTTTGTTGATGGGGgtaaaaatta ... ttattttcagGTGGAAAACAATTTGTGCACTCCAAAAAATGGCGAGATTCTGGTTGCTTCT
EST:
gi|298179026|gb|HO024761.1|HO024761EST: ATGTCCCACAGACTGAGGAGGCTAGGACAGAGGCTATTTTGTTGATGGGG GTGGAAAACAATTTGTGCACTCCAAAAAATGGCGAGATTCTGGTTGCTTCT
genomic: ATGTCCCACAGACTGAGGAGGCTAGGACAGAGGCTATTTTGTTGATGGGGgtaaaaatta ... ttattttcagGTGGAAAACAATTTGTGCACTCCAAAAAATGGCGAGATTCTGGTTGCTTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagcatttgaagaacttaacattattttcttactggaattttgtttattttcagGTGGAAAACAATTTGTGCACTCCAAAAAATGGCGAGATTCTGGTTGCTTCTACTCAAGACTTTTTAACATCTTCCTTTCTCATAACCAGGAAAGATACTT
ttcttac putative branch site (score: 2)
ttttgtttattttc putative PPT
ttaacattattttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacatattttaatattgtgtgatttgttcaattgagtgtatggtttaagcatttgaagaacttaacattattttcttactggaattttgtttattttcagGTGGAAAACAATTTGTGCACTCCAAAAAATGGCGAGATTCTGGTTGCTTCTACTCAAGACTTTTTAACATCTTCCTTTCTCATAACCAGGAAAGATACTT
- - - - - - - -tgtgtga
- - - - - - - - - - - - - - - - tgagtgt
- - - - - - - - - - - - - - - - - - - - - - - - gcatttg