Sequence
atgc intronic sequence ATGC exonic sequencegttaatataatttcatctgctcaaatgattccatgctgtaaagttttattattttcttttcggtatccgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGCCTTATAGAAAAGAAACTTAAAAATCGAATTCAATGGAA
Basic information
species | Glycine max |
transcript | GLYMA12G09860.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G09860.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g06200.2 (Oryza sativa), 3'ss of exon 4
--------------------gttaatataatttcatctgctcaaatgattccatgctgtaaagttttattattttcttttcggtatccgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGCCTTATAGAAAAGAAACTTAAAAATCGAATTCAATGGAA
|| | || | |||| | | | | || ||| ||| || ||| | | | |||||| ||||| ||| | |||||||| || || ||||| ||||||||||| || || ||||||||||| || || || || | |||||
gttaatatttccttctgtttttttctcatatcctgtttgctaacacgcctttattttgtcaagctta--tatgtatgtaaaatgttttgcagGTACAAAAAAGGCGTATATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAA
upper sequence: GLYMA12G09860.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G333591_T01 (Zea mays), 3'ss of exon 6
-----------------------gttaatataatttcatctgctcaaatgattccatgctgtaaagttttatta------ttttcttttcggtatccgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGCCTTATAGAAAAGAAACTTAAAAATCGAATTCAATGGAA
||| | || | | || | |||| | | || |||| ||| | | | | | | ||||| || || ||| | |||||||| || || ||||||||||||||||| || || ||||||||||| ||||| || || | |||||
gatgatattgatgttgactagaggttggtgct-ttccttttggtaccttgatccagtcatggtttcttttgttaaacatatgcatatatagcttttttcagGTACAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAGAACAACATCCGTTGGAA
upper sequence: GLYMA12G09860.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G829408_T01 (Zea mays), 3'ss of exon 6
-------------------------gttaatataatttcatctgctcaaatgattccatgctgtaaagttttattat-----tttcttttcggtatccgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGCCTTATAGAAAAGAAACTTAAAAATCGAATTCAATGGAA
||| | |||| | | | |||| | | || |||| ||| | | | | | ||||| || || ||| | |||||||| || || ||||||||||||||||| || || ||||||||||| ||||| || || | |||||
cagatgatattgatgttgactagaggttggtgc--tttccttttggtacttgatccagtcatggtttcttttgttaaacatatgcgtatatagctttttcagGTACAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAGAACAACATCCGTTGGAA
upper sequence: GLYMA12G09860.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G029735_T01 (Zea mays), 3'ss of exon 3
-----------------------gttaatataatttcatctgctcaaatgattccatgctgtaaagttttatta------ttttcttttcggtatccgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGCCTTATAGAAAAGAAACTTAAAAATCGAATTCAATGGAA------------
||| | || | | || | |||||| | || |||| ||| | | | | | | ||||| | || ||| | |||||||| || || ||||||||||||||||| || | | | || | | || || |||
gatgatattgatgttgactagaggttggtgct-ttccttttggtaccttgattcagtcatggtttcttttgttaaacatatgcatatatagcttttttcagGTATAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACAT-CACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAG
upper sequence: GLYMA12G09860.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G22220.2 (Arabidopsis thaliana), 3'ss of exon 4
--------gttaa--tataatttcatctgctcaaatgattccatgctgtaaagttttattattttcttttcggtatccgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGCCTTATAGAAAAGAAACTTAAAAATCGAATTCAATGGAA
|| | | || || | | | | ||| | | |||| || || | | | | | || |||||| |||||||| ||||||||||||||||| ||||| | ||||| || || | ||||| |||| ||||| || | ||||| |||||
gtgacatatttgaactctagactcccatattgatgt-attactttctgtcaaacttagctgtatgttcct--gttgatgcagGTACAAAAGAGAAGGATATATGATATAACCAATGTGTTAGAAGGAATAGGTTTGATAGAGAAGACGCTTAAGAACAGGATTCAGTGGAA
upper sequence: GLYMA12G09860.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0080g01110.t01 (Vitis vinifera), 3'ss of exon 4
gttaatataatttcatctgctcaaatgattccatgctgtaaagttttattatttt---cttttcggtatccgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGCCTTATAGAAAAGAAACTTAAAAATCGAATTCAATGGAA
| ||| | | | ||| || | || ||| | | | | || | |||| | | ||||| || |||||| | |||||||| ||||||||||| |||||||| ||||| || || || ||||| | || ||| ||||||| |||||
-gtgctattttatatctaacgcaatatatcctgtggcataacatcctgtcaattgaaacgtttccattatcacagGTACAGAAGAGGCGTATATATGACATAACAAATGTCCTTGAAGGAATTGGTCTCATTGAGAAGAAGTTGAAGAATAGAATTCAGTGGAA
upper sequence: GLYMA12G09860.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S38_356V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------gttaatataatttcatctgctcaaatgattccatgctgtaaagttttattattttcttttcggtatccgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGCCTTATAGAAAAGAAACTTAAAAATCGAATTCAATGGAA
||| |||| | | ||| | || ||| || | | | | | || ||| || ||||| ||||||||||||||||||||||| || ||||| | || || ||||| | || || ||||| || || |||||||| ||||||
tatgtagcgctgttatcctttcatttatttcaagtaa-ataactacctctttttaagctgttctctgacatcagac---gatgtacaatcttgggtttcaccagGTACAAAAGAGGAGGATATATGATATTACCAATGTATTGGAGGGAATTGGGTTAATTGAGAAGAAGCTAAAGAATCGAATCAGATGGAAMapped 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|7588272|gb|AW704071.1|AW704071EST: AAGCTGAGGATGGTATCCTTGATCTGAATAAAGCTGCTGACACATTAGAG GTGCAAAAGATGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGC
genomic: AAGCTGAGGATGGTATCCTTGATCTGAATAAAGCTGCTGACACATTAGAGgttaatataa ... gtatccgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctcaaatgattccatgctgtaaagttttattattttcttttcggtatccgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGCCTTATAGAAAAGAAACTTAAAAATCGAATTCAATGGAA
tgtaaagttttattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaatataatttcatctgctcaaatgattccatgctgtaaagttttattattttcttttcggtatccgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGCCTTATAGAAAAGAAACTTAAAAATCGAATTCAATGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA