Sequence
atgc intronic sequence ATGC exonic sequence...taaattttaaagttgagcataatcaccatattattactgaagttatcatctaatattctgtaattattcctccattgggagctggatgcttttattgcagTTCTCTTGGTCAGAACCTGGCAACAAGTACCTATGTTTGGGAAATCAGTTTTGCAGTTTTCATTTCTGTATCTGGTTTGGTATTATTTTCATTCCTCATT
Basic information
species | Glycine max |
transcript | GLYMA14G31940.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G31940.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G53130.1 (Arabidopsis thaliana), 3'ss of exon 5
taaattttaaagttg--agcataatcaccat-attattactgaagttatcatctaatattctgtaattattcctccattgggagctggatgcttttattgcagTTCTCTTGGTCAGAACCTGGCAACAAGTACCTATGTTTGGGAAATCAGTTTTGCAGTTTTCATTTCTGTATCTGGTTTGGTATTATTTTCATTCCTCATT
||| || || |||| ||| | || | ||||| | | || | | || || || || ||| | | | | |||||| || ||||||||||| ||||||||| ||| ||||||||||| |||| || || ||||||||| | | || |||| || || || ||| | |||
-gtattgagaatttatcagcaaaattttctccgtttcttatgaagaaaagtttcaacactaagttcttgcatctttgtt-----ctg--ttttcgtgatccagTTCGCTCGGTCAGAACCTTAAAACAAGTACATATATTTGGGAAATCTGTTTCGCGGTGTTCATTTCTATTGCGGGGCTGGTTTTGTTCTCCTTCTTGATT
upper sequence: GLYMA14G31940.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv16s0050g02560.t01 (Vitis vinifera), 3'ss of exon 5
-taaattttaaagttgagcataatcaccatattattactgaagtt-atcatctaatattctgtaattattcctccattgggagctggatgcttttattgcagTTCTCTTGGTCAGAACCTGGCAACAAGTACCTATGTTTGGGAAATCAGTTTTGCAGTTTTCATTTCTGTATCTGGTTTGGTATTATTTTCATTCCTCATT
|| ||| | | | | ||| | || || | || | |||| || | | |||||| ||| || | | | ||| |||||||||||||||||| ||||| |||||| |||||||| |||||||| | |||||||| |||||||| | ||||| ||||| ||||||||||| || |||
tctctttgtaatgataaatgcatacacttttggttttcttactttgagcatc--atttgtgtttattattgtggtattttatacttggtacattttttgcagTTCTCTTGGTCAAAACCTCAAAACAAGCACCTATGTCTGGGAAATTTGCTTTGCAGTGTTCATTTCCATCTCTGGCTTGGTTTTATTTTCATTTCTTATTMapped 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|193425311|gb|FK387828.1|FK387828EST: TTTCCACAAAAATTCTTTTACTGCTTTTGGTGGGGCCTAAAAAATTTGAG TTCTCTTGGTCAGAACCTGGCAACAAGTACCTATGTTTGGGAAATCAGTTT
genomic: TTTCCACAAAAATTCTTTTACTGCTTTTGGTGGGGCCTAAAAAATTTGAGgtgcacttcc ... tttattgcagTTCTCTTGGTCAGAACCTGGCAACAAGTACCTATGTTTGGGAAATCAGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatctaatattctgtaattattcctccattgggagctggatgcttttattgcagTTCTCTTGGTCAGAACCTGGCAACAAGTACCTATGTTTGGGAAATCAGTTTTGCAGTTTTCATTTCTGTATCTGGTTTGGTATTATTTTCATTCCTCATT
atctaat putative branch site (score: 3)
cttttatt putative PPT
taatattctgtaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaattttaaagttgagcataatcaccatattattactgaagttatcatctaatattctgtaattattcctccattgggagctggatgcttttattgcagTTCTCTTGGTCAGAACCTGGCAACAAGTACCTATGTTTGGGAAATCAGTTTTGCAGTTTTCATTTCTGTATCTGGTTTGGTATTATTTTCATTCCTCATT
- - - - - - - - - - - tcaccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgggag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggatgct