Sequence
atgc intronic sequence ATGC exonic sequencegtaattgtgattctgcccgttattattttcctaatcaaagttatccttttattttatttgcaatagtttattacctttttcctcattttccccatcatcatatatgaattactagGAAATGCTCCCCTCACTGCGGTTCAACTTCTATGGGTCAACATGATCATGGACACTCTTGGAGCACTTGCACTAGCCACTGAACCTCCTAACGATGAGTT
Basic information
species | Glycine max |
transcript | GLYMA04G04810.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G04810.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g10640.1 (Oryza sativa), 3'ss of exon 5
gtaattgtgattctgcccgttattattttcctaatcaaagttatccttttattttatttgcaatagtttattacctttttcctcatt-ttccccatcatcatatatgaattactagGAAATGCTCCCCTCACTGCGGTTCAACTTCTATGGGTCAACATGATCATGGACACTCTTGGAGCACTTGCACTAGCCACTGAACCTCCTAACGATGAGTT
|| || | || || || | | | | | |||| || ||| || | | | ||| | | | || | | ||| | |||||| || ||||| || ||||| || ||||| ||||||||||||||||| || |||||||| ||| | || ||||||||||| |||||||| |
---------------taaactaacataaaatttattaatgtggaaaatcaagaatttcctagtttgtttcataacttactcttgactgttctttgtacttctgcttggcattc-agGGAGTGCTCCTCTTACTGCTGTCCAACTGCTCTGGGTTAACATGATCATGGACACACTAGGAGCACTGGCATTGGCAACTGAACCTCCAAACGATGAACT
upper sequence: GLYMA04G04810.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G27770.1 (Arabidopsis thaliana), 3'ss of exon 5
-gtaattgtgattctgcccgttattattttcctaatcaaagttatccttttattttatttgcaatagtttattacctttttcctcattttccccatcatcatatatgaattactagGAAATGCTCCCCTCACTGCGGTTCAACTTCTATGGGTCAACATGATCATGGACACTCTTGGAGCACTTGCACTAGCCACTGAACCTCCTAACGATGAGTT
|| || | | | ||||| || || | ||||| | || | | | || | | || ||| | | | || | | | | | || | |||||| || || || ||||| || ||||| || ||||| |||||||| |||||||| ||||||||||| || ||||| |||||||| || | || || |
gttagttcccaacccacat-ttatttttctcttgttcaaaag-----actaatctcctcagggattgca-actaacttctctgttacattgacactaactac-tgtgggtc-tcagGAAACGCGCCTCTGACTGCTGTCCAACTACTGTGGGTTAACATGATAATGGACACACTTGGAGCACTCGCGCTAGCGACTGAACCACCACAGGACGACCT
upper sequence: GLYMA04G04810.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g09150.t01 (Vitis vinifera), 3'ss of exon 5
gtaattgtgattctgcccgttattattttcctaatcaaagttatcctttt--attttatttgcaatagtttattacctttttcctcattttccccatcatcatatatgaattactagGAAATGCTCCCCTCACTGCGGTTCAACTTCTATGGGTCAACATGATCATGGACACTCTTGGAGCACTTGCACTAGCCACTGAACCTCCTAACGATGAGTT
||| | || ||| | | || || | ||||| |||| |||| || ||| | | ||| | | |||| | || || | ||||||||||||||| || |||||||| ||||| |||||||||||||| ||||| || || |||||||||||||| || |||||||||||||| ||||||||
gtatata-gaccctgatgttggctcttgcccattctgtatttatcattttgaatttctgttttgcatgttattcatcttcacctttgttttttgggttg----atgtgtggtctcagGAAATGCTCCCCTGACCGCGGTTCAGCTTCTGTGGGTCAACATGATTATGGATACACTGGGAGCACTTGCACTGGCTACTGAACCTCCTAATGATGAGTTMapped 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|6566478|gb|AW234123.1|AW234123EST: TGTAAATGTTGTTGCTTTGATCGTCAATTTCTCTTCTGCTTGTTTGACTG GAAATGCTCCCCTCACTGCGGTTCAACTTCTATGGGTCAACATGATCATGG
genomic: TGTAAATGTTGTTGCTTTGATCGTCAATTTCTCTTCTGCTTGTTTGACTGgtaattgtga ... gaattactagGAAATGCTCCCCTCACTGCGGTTCAACTTCTATGGGTCAACATGATCATGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatagtttattacctttttcctcattttccccatcatcatatatgaattactagGAAATGCTCCCCTCACTGCGGTTCAACTTCTATGGGTCAACATGATCATGGACACTCTTGGAGCACTTGCACTAGCCACTGAACCTCCTAACGATGAGTT
atcatatatgaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattgtgattctgcccgttattattttcctaatcaaagttatccttttattttatttgcaatagtttattacctttttcctcattttccccatcatcatatatgaattactagGAAATGCTCCCCTCACTGCGGTTCAACTTCTATGGGTCAACATGATCATGGACACTCTTGGAGCACTTGCACTAGCCACTGAACCTCCTAACGATGAGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA