Sequence
atgc intronic sequence ATGC exonic sequence...aaaattatttaattgtattagggttaactctactcatttatctttttactgtatttttggtttgagactctggccaactgttcctattcacaattttcagGTTTATTGATACCTTTGGTACCCATATAATTGTTGGTATGAAAATGGGTGGAAAAGATGTAATATATTTGAAGCAGCAGCACTCATCAACTCTCCAACCT
Basic information
species | Glycine max |
transcript | GLYMA16G00440.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G00440.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G435034_T01 (Zea mays), 3'ss of exon 2
aaaattatttaattgtattag-ggttaactctactcatttatctttttactgtatttttggtttgagactct--ggccaactgttcctattcacaa-ttttcagGTTTATTGATACCTTTGGTACCCATATAATTGTTGGTATGAAAATGGGTGGAAAAGATGTAATATATTTGAAGCAGCAGCACTCATCAACTCTCCAACCT
| |||||| | | | | || | ||| | | || ||| || | ||| | | | ||| | | | |||||||||||| | | ||||| || |||||| ||||||| | || |||||||| ||||||||||| ||||||||||| || || |||||||| | ||| ||
----cttactaattgaactgtcagcttaccattttcaccgaattattctctgagttaaaatgtcatcactacaggacttaaagtttaattgcttggctcttcagGTTTATTAAAAAATTTGGCACTCATATAGTTGTTGGCCTAAAGATGGGTGGGAAAGATGTAATTTATTTGAAGCAACAACATTCATCAACCTTGCAAGCT
upper sequence: GLYMA16G00440.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G028758_T01 (Zea mays), 3'ss of exon 2
----------aaaattatttaattgtattagggttaactctactcatttatctttttactgtatttttggtttgagactctggccaactgttcctattcacaattttcagGTTTATTGATACCTTTGGTACCCATATAATTGTTGGTATGAAAATGGGTGGAAAAGATGTAATATATTTGAAGCAGCAGCACTCATCAACTCTCCAACCT
|||| |||| |||||| || | || | | | || | | | |||| ||| || || | | || || | || |||||||||||||||||| ||||| || || ||| |||| ||| | |||||||| || |||||||| ||||||||||| || || || || |||| | |||||
gtttctcagctaaatggttta-ttgtataag--tagacgttgcaaaggaatatactagttatattgc--acctgaacctttg----attcttgctgctt-cacttttcagGTTTATTGATAAGTTTGGAACACACATAGTTGTCGGTGTAAAAATGGGAGGGAAAGATGTTATATATTTGAAACAACAACATTCGTCAAGCTTGCAACCA
upper sequence: GLYMA16G00440.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0035g01040.t01 (Vitis vinifera), 3'ss of exon 3
aaaattatttaattgtattagggttaactctactcatttatctttttactgtatttttggtttgagactctggccaactgtt-------cctattcacaattttcagGTTTATTGATACCTTTGGTACCCATATAATTGTTGGTATGAAAATGGGTGGAAAAGATGTAATATATTTGAAGCAGCAGCACTCATCAACTCTCCAACCT
||||| | || | | | | || | | | | | ||| | | | || || | || | || | || | || |||||||||||| || ||||| |||||||| || |||||| |||| ||||| || || |||||||||||| | | |||||||| | ||| |||| ||||||
---attatctctttcttctt---tcacctatgtttggt-gttggtataccatgctcaagcttgagaaccataatgaatttttgagatgattttctctgtaattccagGTTTATTGAAACATTTGGCACCCATATTATAGTTGGTGTGAAGATGGGCGGGAAGGATGTAATATATGTTAGACAGCAGCATGCTTCACCTCTTCAACCTMapped 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|208253541|gb|GE057213.1|GE057213EST: CACGTTAAAAAAGCTGTACCATCATCATGGGACCCTCCTGCATTAGCAAG GTTTATTGATACCTTTGGTACCCATATAATTGTTGGTATGAAAATGGGTGG
genomic: CACGTTAAAAAAGCTGTACCATCATCATGGGACCCACCTGCATTAGCAAGgtgaattgag ... caattttcagGTTTATTGATACCTTTGGTACCCATATAATTGTTGGTATGAAAATGGGTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttactgtatttttggtttgagactctggccaactgttcctattcacaattttcagGTTTATTGATACCTTTGGTACCCATATAATTGTTGGTATGAAAATGGGTGGAAAAGATGTAATATATTTGAAGCAGCAGCACTCATCAACTCTCCAACCT
ttttc CT-rich tract
tattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaattatttaattgtattagggttaactctactcatttatctttttactgtatttttggtttgagactctggccaactgttcctattcacaattttcagGTTTATTGATACCTTTGGTACCCATATAATTGTTGGTATGAAAATGGGTGGAAAAGATGTAATATATTTGAAGCAGCAGCACTCATCAACTCTCCAACCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - -ctactca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttcc