Sequence
atgc intronic sequence ATGC exonic sequence...tatttatctaaatagagactggttcaatcgtactaaatttggatatcatattctcataacacaagactaatgttgttcttattttttattttttttgcagAAGTTAGTAATCAAATGTTAGAGCTCTATGAACAAAATCGAATGCCACCTTCCAATGATGTCGAAGGAGGTGGGACTTCCAATCGGACCACTGCAAAAGC
Basic information
species | Glycine max |
transcript | GLYMA15G41040.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G41040.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 6
--tatttatctaaat-----agagactggttcaatcgtactaaatttggatatcatattctcataacacaagactaatgttgttcttattttttattttttttgcagAAGTTAGTAATCAAATGTTAGAGCTCTATGAACAAAATCGAATGCCACCTTC-CAATGATGTCGAAGGAGGTGGGACTTCCAATCGGACCACTGCAAAAGC---
|| |||| ||| | | | || ||| | | ||| | | |||| | | | ||| |||| || | | || || ||||||||||| ||||||||||| ||||| ||||| ||||| | ||| | ||| | | | ||| || || | ||| | |||| | |
tatacttatttaactttttgataatacaatttgatcatgacacattcctttctgg-gttcttgttaaatcaga-taataatgcatgtctcccttgatt-----gcagAAGTTAGCAATCAAATGTTGGAGCTGTATGAGCAAAACTGTGCAGCACAGGCACAACCGTCCC-ATGGAAATGAAGCT---GAAGGGAGCTCTGCTAGTGTTCC
upper sequence: GLYMA15G41040.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0027g01670.t01 (Vitis vinifera), 3'ss of exon 5
---------tatttatctaaatagagactggttcaatcgtactaaatttggatatcatattctcataacacaagactaatgttgttcttattttttattttttttgcagAAGTTAGTAATCAAATGTTAGAGCTCTATGAACAAAATCGAATGCCACCTTCCAATGATGTCGAAGGAGGTGGGACTTCCAATCGGACCACTGCAAAAGC
| | | | | | || || ||| || | | | | || | ||| ||| ||||| || | ||| ||| |||| ||| || |||||||||||||| |||||||| |||||||||||| |||||||||| | | |||| | || | | | |||| |
aagggagggtgatgaaaagatcccacagtgatt-aattgttttggaactactttatgaatatttatatcaccct-ttaatggtg-----gtcatttgtttctttt--agAGGTCAGTAATCAAATGTTGGAGCTCTACGAACAAAATCGAGTGCCACCTTCTCAAGGCAGTGAAGTTGAAGGAAGTGTTGGAGGTGGGGCTGCTCATCGMapped 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|120530094|gb|EH258228.1|EH258228EST: GGAGAAGGTCTGGTGGCAAGAGTTTGATGTCACTCCACGCCAATTGGAGG -AGTTAGTAATCAAATGTTAGAGCTCTATGAACAAAATCGAATGCCACCTT
genomic: GGAGAAGGTCTGGTGGCAAGAGTTTGATGTCACTCCACGCCAATTGGAGGgttggtgtct ... ttttttgcagAAGTTAGTAATCAAATGTTAGAGCTCTATGAACAAAATCGAATGCCACCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatattctcataacacaagactaatgttgttcttattttttattttttttgcagAAGTTAGTAATCAAATGTTAGAGCTCTATGAACAAAATCGAATGCCACCTTCCAATGATGTCGAAGGAGGTGGGACTTCCAATCGGACCACTGCAAAAGC
gactaat putative branch site (score: 2)
ttgttcttatttttta CT-rich tract
aagactaatgttgttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatttatctaaatagagactggttcaatcgtactaaatttggatatcatattctcataacacaagactaatgttgttcttattttttattttttttgcagAAGTTAGTAATCAAATGTTAGAGCTCTATGAACAAAATCGAATGCCACCTTCCAATGATGTCGAAGGAGGTGGGACTTCCAATCGGACCACTGCAAAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - -actggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacacaag