Sequence
atgc intronic sequence ATGC exonic sequence...tatcttaattctggtcaactgagtaatcttactgtttgcattcaattttaaacaatgcatacatgtacggggtctcacttttggcttctacatgtctcagGTCGTTCCTAGATGGTATGAGCATTGGACTTCAAACAAGGTATATGATGGAGACATGATTGTTCTTCAAGGCCAAGAGAAAATCTTCCTTTCAGAAACCA
Basic information
species | Glycine max |
transcript | GLYMA12G08740.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G08740.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g05310.1 (Oryza sativa), 3'ss of exon 5
tatcttaattctggtcaactgagtaatcttactgtttgcattcaattttaaacaatgcatacatgtacggggtctcactt-ttggcttctacatgtct------cagGTCGTTCCTAGATGGTATGAGCATTGGACTTCAAACAAGGTATATGATGGAGACATGATTGTTCTTCAAGGCCAAGAGAAAATCTTCCTTTCAGAAACCA
|||| || || | | ||| | | | | | | | | || || | | | | ||| | || |||||| ||| | ||| | || ||| ||||||||||||||||||||||||| ||| |||||||| || ||||| ||||| ||||| |||||||| || ||| | || | | | |
------aattagagtgaattttatgctctcattatatccgaa-agtataaagtaaaaccctgaatcccctgttcttatacatttgcttctttgtgtatgtgatgcagCTTGTCCCTCGATGGTATGAGCATTGGACTTCAAATTTGGTCTATGATGGTGATATGATAGTTCTGCAAGGGCAAGAGAAGATTTTCTTGTCTGCATCGA
upper sequence: GLYMA12G08740.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G339563_T01 (Zea mays), 3'ss of exon 5
--tatcttaattctggtcaactgagtaatcttactgtttgcattcaattttaaacaatgcatacatgtacggggtctcacttttggcttctacatgtctcagGTCGTTCCTAGATGGTATGAGCATTGGACTTCAAACAAGGTATATGATGGAGACATGATTGTTCTTCAAGGCCAAGAGAAAATCTTCCTTTCAGAAACCA
|| || | | || | ||| | ||| | ||| || || | | | | | | |||| | || || | |||||| |||||||||| |||||||||||||| ||| |||||||| || ||||| |||||||||||||| ||||| || ||||| | | |||||
cctactgtaggcatatattattggcagagtttattacttg-gtcatgtttgaatttatatgtgtacagtcaaatgttgatagcttctttct-cttggtgtagCTTGTTCCTCGATGGTATGAACATTGGACTTCAAATTTGGTCTATGATGGCGATATGATCGTTCTTCAAGGCCAGGAGAAGATTTTCCTAGCTGCAACCA
upper sequence: GLYMA12G08740.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G44880.1 (Arabidopsis thaliana), 3'ss of exon 5
tatcttaattctggtcaactgagtaatcttactgtttgcattcaattttaaacaatgcatacatgtacggggtctcacttttggcttctacatgtctcagGTCGTTCCTAGATGGTATGAGCATTGGACTTCAAACAAGGTATATGATGGAGACATGATTGTTCTTCAAGGCCAAGAGAAAATCTTCCTTTCAGAAACCA
|||| | |||| | || | ||| | ||| |||| || | ||| | | ||| |||| || || ||||||||||| || |||||||| ||| || ||||| ||||||||||| || |||||||| ||||||||| | ||||| | || | |
----------------------gtaaaacaaac-tttgattccatctctaatccgattttac---tacgtaaattcttctgaagctgttccttgtt--agGTTGTACCAAGATGGTATGAACACTGGACTTCGAACTTAGTCTATGACGGAGACATGATCGTACTTCAAGGACAAGAGAAAGTATTCCTCGCTAAATCAA
upper sequence: GLYMA12G08740.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0061g00790.t01 (Vitis vinifera), 3'ss of exon 5
tatcttaattctggtcaactgagtaatcttactgtttgcatt-caattttaaacaatgcatacatgtacggggtc-tcacttttggcttctacatgtctcagGTCGTTCCTAGATGGTATGAGCATTGGACTTCAAACAAGGTATATGATGGAGACATGATTGTTCTTCAAGGCCAAGAGAAAATCTTCCTTTCAGAAACCA
||| || | || | | || | | || | || | ||| | || || | | || | ||| |||| || | ||| ||||| |||||||||||| ||||||| ||||||||||| |||||||||||||||||||||||||| ||||| || |||||||| || ||||||||| | | |
catcagtgaacttcttaa--aaattatgtcataactttctttactgtttatatcattggacatcagtgaatttccctcatatttgatttgtggctgtggcagGTGGTTCCTAGATGGCATGAGCACTGGACTTCAAATAAGGTATATGATGGAGACATGATTGTCCTTCAGGGTCAAGAGAAGATATTCCTTTCAAAGTCAA
upper sequence: GLYMA12G08740.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ20275 (Selaginella moellendorffii), 3'ss of exon 5
tatcttaattctggtcaactgagtaatcttactgtttgcattcaattttaaacaatgcatacatgtacggggtctcacttttggcttctacatgtctcagGTCGTTCCTAGATGGTATGAGCATTGGACTTCAAACAAGGTATATGATGGAGACATGATTGTTCTTCAAGGCCAAGAGAAAATCTTCCTTTCAGAAACCA
|| |||| || | | | ||| | || || ||||| | || || |||||||| ||||| || || ||||| |||||||| |||||||||||||||||||| | || | || |
------------------------------------------------------------------------gttcttttttaactctctcgtattgcagCTGGTACCACGATGGCACGAACACTGGACTTCCAACAAAGTTTACGATGGCGACATGATAGTTCTTCAAGGCCAAGAGAAGAAGTTTTTGGCAACAGGAGMapped 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|16349342|gb|BI974937.1|BI974937EST: GTGCTCGAAACTTCTTCCAGTTCTCAGTGCCAGGGCCAGCCTGGTGGCAA GTCGTTCCTAGATGGTATGAGCATTGGACTTCAAACAAGGTATATGATGGA
genomic: GTGCTCGAAACTTCTTCCAGTTCTCAGTGCCAGGGCCAGCCTGGTGGCAAgtaagatttc ... catgtctcagGTCGTTCCTAGATGGTATGAGCATTGGACTTCAAACAAGGTATATGATGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttaaacaatgcatacatgtacggggtctcacttttggcttctacatgtctcagGTCGTTCCTAGATGGTATGAGCATTGGACTTCAAACAAGGTATATGATGGAGACATGATTGTTCTTCAAGGCCAAGAGAAAATCTTCCTTTCAGAAACCA
gtctcac putative branch site (score: 3)
cttctac putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatcttaattctggtcaactgagtaatcttactgtttgcattcaattttaaacaatgcatacatgtacggggtctcacttttggcttctacatgtctcagGTCGTTCCTAGATGGTATGAGCATTGGACTTCAAACAAGGTATATGATGGAGACATGATTGTTCTTCAAGGCCAAGAGAAAATCTTCCTTTCAGAAACCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA