Sequence
atgc intronic sequence ATGC exonic sequence...tcttgacttcacattcaagcagttactttgttatctgttccaaaaatacacccttaatttggccttcagttatgaaatttctttttgtactttcatgcagGCATTTGGTAGAACACCACTTACCAGCGTAAGTCCAAAGAAGACATGGGAGGGTACTATTATAGGCTTTTGTGGGTGTATAATTACTTCTGTTGTACTGT
Basic information
species | Glycine max |
transcript | GLYMA11G30030.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G30030.3 (Glycine max), 3'ss of exon 5
lower sequence: AT3G60620.1 (Arabidopsis thaliana), 3'ss of exon 4
tcttgacttcacattcaagcagttactttgttatctgttccaaaaatacacccttaatttggccttcagttatgaaatttctttttgtactttcatgcagGCATTTGGTAGAACACCACTTACCAGCGTAAGTCCAAAGAAGACATGGGAGGGTACTATTATAGGCTTTTGTGGGTGTATAATTACTTCTGTTGTACTGT
|| | | | || ||| | || | | | || || | || | | ||||||||||||||||||| || |||| ||| | |||||||||||||||||||| || || || ||| || ||| ||||| | | | || |||| |
----------------------gtatgtatcttttcagggcatgcatatagtctcgcaagaacttctcctggctgaagttaatcaactaatgt--tgcagGCATTTGGTAGAACTCCTCTTATTAGCATTAGTCCAAAGAAGACATGGGAAGGAGCTTTTGCAGGACTTGTTGGTTGTATTTCCATTACCATTTTACTCT
upper sequence: GLYMA11G30030.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv15s0048g00240.t01 (Vitis vinifera), 3'ss of exon 4
--tcttgacttcacattcaagcagttactttgttatctgttccaaaaatacacccttaatttggccttcagttatgaaatttctttttgtactttcatgcagGCATTTGGTAGAACACCACTTACCAGCGTAAGTCCAAAGAAGACATGGGAGGGTACTATTATAGGCTTTTGTGGGTGTATAATTACTTCTGTTGTACTGT
|||| | || | | | |||| | | || | ||| | | || || || || | | || |||| || | | ||||||||||||||| |||||||||| |||| | ||||||||||||||||||||||| |||| |||||| |||| |||||| ||||||||| || |||
attctttatgccattattagaacttaacttggatgact-tcttaaattcataatgttctctttaccaacatgaactgagattatttt-gttttgtaatgcagGCATTTGGTCGAACACCACTCACCAATATTAGTCCAAAGAAGACATGGGAGGGAGTTATTGCAGGCTTAGGTGGTTGTATAGCCACTTCTGTTATATTGTMapped 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|21887057|gb|BQ740270.1|BQ740270EST: CCATAAGCAGCGTAATTGCAGCTGATACATTTGCATTTCTTGGTGGCAAG GCATTTGGTAGAACACCACTTACCAGCGTAAGTCCAAAGAAGACATGGGAG
genomic: CCATAAGCAGCGTAATTGCAGCTGATACATTTGCATTTCTTGGTGGCAAGgtatatagac ... tttcatgcagGCATTTGGTAGAACACCACTTACCAGCGTAAGTCCAAAGAAGACATGGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacacccttaatttggccttcagttatgaaatttctttttgtactttcatgcagGCATTTGGTAGAACACCACTTACCAGCGTAAGTCCAAAGAAGACATGGGAGGGTACTATTATAGGCTTTTGTGGGTGTATAATTACTTCTGTTGTACTGT
ccttaat putative branch site (score: 4)
tttctttttgtacttt putative PPT
ttatgaaatttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttgacttcacattcaagcagttactttgttatctgttccaaaaatacacccttaatttggccttcagttatgaaatttctttttgtactttcatgcagGCATTTGGTAGAACACCACTTACCAGCGTAAGTCCAAAGAAGACATGGGAGGGTACTATTATAGGCTTTTGTGGGTGTATAATTACTTCTGTTGTACTGT
- - -acttcac
- - - - - - -ttcaagc
- - - - - - - - - - - - - - - - - ctgttcc
- - - - - - - - - - - - - - - - - - - - -aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - caccctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccttca