Sequence
atgc intronic sequence ATGC exonic sequence...ttgctatctgaaatcaataattaatttgcatgctagatatgtctttatgctgattggtcatttgtctgcaatgctaaagtctatggtttgaatctttgtaGCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGAT
Basic information
species | Glycine max |
transcript | GLYMA18G44460.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 3
ttgctatctgaaatcaataattaatttgcatgctagatatgtctttatgctgattggtcatttgtctgcaatgctaaagtctatggtttgaatcttt-----gtaGCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGAT-
| || || || | | | || ||| ||| || || || ||| | | | ||| | ||| | || |||| ||||||||||||| ||||| ||||| || || |||||||||||||| || || || |||||||| || || ||
cttagattgatttacactatgtcagtggcgcacta--tataatttcatactcatttgctgtaattt----atgttttagtttgctaattcctcctttcataaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
upper sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 2
-ttgctatc-tgaaatcaataattaat-ttgcatgctagat-atgtctttatgctgattggtcatttgtctgcaatgctaaagtctatggtttgaatctttgtaGCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGAT-
| |||| | | | | ||| || | | | | || | ||| | || ||||| ||| || | | || | | | | |||||||||| |||||||||||| | || ||||| |||||||| ||||| ||||||||||||||||| || ||
ttgaatatcgtcgagtttactattgatactattcatttgttgatatttttggtgttgttacctatttgct--caacgcct---tgttgggcactattgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG
upper sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S13_321V6.1 (Physcomitrella patens), 3'ss of exon 2
-ttgctatc-tgaaatcaataattaatttgcatgctagatatgtctttatgctgattggtcatttgtctgcaatgctaaagtctatggtttgaatctttgtaGCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGAT-
| | | || |||| ||| || | || | || | | |||| | || | | |||||| || ||| | | || |||||||||| |||||||| ||| | |||||||| || ||||| ||||| || ||||||||||| || || ||
ctggttgtcatgaagacaacttgtactgtgtttctcaggctgatactgttgcttttgcttcttattcacccaatgcgttggt---gggtattgttgttcacagCGTTTTGCAGCTGTTATCATGCGAATCAGGGAGCCTAAAACAACTGCTCTTATTTTTGCATCCGGTAAAATGMapped 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|120494436|gb|EH222603.1|EH222603EST: GAGCTTAAATCAATTGCACTTCAAGCTCGTAATGCAGAATACAATCCCAA GCGCTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCAC
genomic: GAGCTTAAATCAATTGCACTTCAAGCTCGTAATGCAGAATACAATCCCAAggtaaatttt ... aatctttgtaGCG-TTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgctgattggtcatttgtctgcaatgctaaagtctatggtttgaatctttgtaGCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGAT
tgctaaa putative branch site (score: 2)
tctttgt putative PPT
tttgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgctatctgaaatcaataattaatttgcatgctagatatgtctttatgctgattggtcatttgtctgcaatgctaaagtctatggtttgaatctttgtaGCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
-tgctatc
- - - - - - - - - - - - - -gcatgct
- - - - - - - - - - - - - - - - - - - - - - - - gctgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtctatg