Sequence
atgc intronic sequence ATGC exonic sequencegtaacattgatgtgctgtaacttacatgtaacttggtttgtttttagaaattaccttgctcatttgttgcaatttttagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCACCAC
Basic information
species | Glycine max |
transcript | GLYMA17G00480.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 11
--gtaacattgatgtgctgta---acttaca-tgtaacttggtttgtttttagaaattaccttg---------ctcatttgttgcaatttttagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCACCAC
|| ||| | | | | ||||||| || | | || ||| | | ||| | ||| | | | || | || | |||||||| || | || | || |||| ||| | ||||| ||||| |||||||| ||||||||||||||||| ||||| |||||||
gtaccactttgttctatttcaccaacttacaatgcattctacttccctttcacctgcttcctgagcacaacatcccatcatctcttttctgaagGTCGTTGAAATTGCAACCAATGCATTGGATGTCTTCAAAAGTGATGCAAAAAAGATGGTAGTTGCACTTGTTGATATGGAGCGTGCCTTTGTCCCACCAC
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 11
------gtaacattgatgtgctgtaacttacatgtaacttggtttgtttttagaaattaccttgctcatttgttgcaatttttagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCACCAC
| || || || | | || ||| | | | || | ||| || | || || | | | | || |||| || || |||||| | || || || | ||| || |||||| | || || ||||| |||||| ||||||||||||||||||||||||| ||||| |
gtaattatgcttttactgctctttcagttgcattt--ttcgtcttactaatagctgtttcttttcttaaataat-cgtcaaccagGTTGTAGCTATAGCAAGTGCCGCACTTGATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTC
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaacattgatgtgctgtaacttacat--gtaacttggtttgtttttagaaattaccttgctcatttgttgcaatttt---tagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCACCAC
|||| | |||| | || ||| | |||| | | | ||| | || | | | || | | || |||| || || |||||| |||| || || | || || |||||| |||| ||||||||||||||||||||||||||||| || || ||||| ||||| |
gtaataatgattttttggtgctttattcagtaatattttatcatttcggtaacagttattcctttctgactaatcatcaaccagGTTGTAGCTATAGCAAGTGCAGCACTTGATGGTTTCAAGAATGAAGCCAAGAAAATGGTGGTTGCACTAGTTGATATGGAACGCGCTTTTGTACCACCTC
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 11
------------------------------------------------------gtaacattgatgtgctgtaacttacatgtaacttggtttgtttttagaaattaccttgctcatttgttgcaattttt------agATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCACCAC
|| || || || | | | | | || || ||| | |||| | |||| |||| || |||| || |||||||||||||| | | || || || | ||||| ||||| | || |||||||| |||||||| |||||||||||||||||||||||||| || |
gtaatcatgctgcaaatgctgcccctttttttttttaagagattccctcctttgatatgtttaatttgatatttttcaagttcaagtttgttggctttt----gtggtacaactcacttgtcataaatttttaaaccagGTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAGAAAATGGTTGTTGCACTTGTTGATATGGAGCGTGCATTTGTTCCCCCTC
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S33_163V6.1 (Physcomitrella patens), 3'ss of exon 11
-----------------------gtaacattgatgtgctgtaacttacatgtaacttggtttgtttt-tagaaattacct--tgctcatttgttgcaat----ttttagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCACCAC
||| || | | ||| | | | | || |||| |||||| || | |||| || || || ||||||| || ||||| |||||||| || || | || | |||||| || |||||||| ||||| || ||||| ||||||||||||||| | ||||| |
gtttgtacaatttcggttccttcgtagtatctgctt-cgataaatgtggtacattatagtgtgttgggctaaaattattcaatgattctttgaggctatgcgtttgcagATTGTTGCCATTGCCAGTTCAGCGCTGGACGAATACAGGGTTGAATCAAAGAAAATGGTTGTTGCTCTTGTTGACATGGAGCGTGCATTTATCCCACCTC
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S109_214V6.1 (Physcomitrella patens), 3'ss of exon 11
-------------------------------------------------------------------gtaacattgatgtgctgtaacttacatgtaacttggtttgtttttagaaattaccttgctcatt--tgttgcaatttt-tagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCACCAC
|| | | | | | | | || || || || || | || ||| | | | | |||| ||| | ||||||| || ||||| | | | || || || | | || | ||| | || |||||||| ||||| || ||||||||||||||||||||| |||| || |
gtgcttatagatttatctctttctactatcaaatgttcactaaattctgtgactgcaaaaattatagttacccatctttttcattgaatttcacacaatgtgcttgggcttacagtattcaatggttactcggtgttataatcctgcagATTGTTGCCATTGCTACTGCTGCGCTGGATGAGTATAGAGCAGAAGCAAAGAAAATGGTTGTTGCGCTTGTTGATATGGAGCGTGCATTTATTCCCCCTCMapped 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|208190948|gb|GD988292.1|GD988292EST: CTGCAAATGCAACGCCTGGTCTTGGAAGGTATCCTCCATTCAAGAGAGAG ATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAA
genomic: CTGCAAATGCAACGCCTGGTCTTGGAAGGTATCCTCCATTCAAGAGAGAGgtaacattga ... caatttttagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgtaacttggtttgtttttagaaattaccttgctcatttgttgcaatttttagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCACCAC
atgtaac putative branch site (score: 3)
ttttt putative PPT
tttgtttttagaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacattgatgtgctgtaacttacatgtaacttggtttgtttttagaaattaccttgctcatttgttgcaatttttagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCACCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG