Sequence
atgc intronic sequence ATGC exonic sequence...tagcaataaactattgcccgtgacttaaaatctaatcaaaatctttactaaagtgcccgactttgagtctattttattaaataagttttgacatgtacagGGCATGATGAACAACTGCTGGTTCAGAGTGAAAACCAATGTGTGCAGGCCCCACAAGGGTGAGATAGGTATAGTGTTTGAACACCCCACCCAACCAGGCA
Basic information
species | Glycine max |
transcript | GLYMA06G11430.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 3
tagcaataaactattgcccgtgacttaaaatctaatcaaaatctttactaaagtgcccgactttgagtctattttattaaataagttttgacatgtacagGGCATGATGAACAACTGCTGGTTCAGAGTGAAAACCAATGTGTGCAGGCCCCACAAGGGTGAGATAGGTATAGTGTTTGAACACCCCACCCAACCAGGCA
| | || || | | ||| | || | |||| || | || || | | || | ||| ||||||||||||||||||||||||||||| ||||| || || ||||||||| |||||||| ||||| || | ||||| || ||||| || || || ||||
---------gtaagcactaagcaccagcaacggcaacgccatccgtttcaacga---cgacgatgtgcttacgtttt--ggttcgtgtgcgtgtgtgcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
upper sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g36480.1 (Oryza sativa), 3'ss of exon 3
tagcaataaactattgcccgtgacttaaaatctaatcaaaatctttactaaagtgcccgactttgagtctattttattaaataagttttgacatgtacagGGCATGATGAACAACTGCTGGTTCAGAGTGAAAACCAATGTGTGCAGGCCCCACAAGGGTGAGATAGGTATAGTGTTTGAACACCCCACCCAACCAGGCA
||| | | | || ||| | | || |||| || | | || ||| || ||| | | | ||||| |||||||||||||||||||||| ||||| || |||||| |||| |||||||||||||| || | ||||| || ||||| || || || || |
---------gtaggtgct--tcattccgtctccggccaaggcgacggc-gatgtagacgacgatgg--caaattcattcgatcggttg-ggtttttgcagGGGATGATGAACAACTGCTGGTTCAAGGTGAAGGTGAACGTGTGCCGGCCGCACAAGGGTGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCCGGGA
upper sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G878558_T01 (Zea mays), 3'ss of exon 3
--------tagcaataaactattgcccgtgacttaaaatc-taatcaaaatctttacta-aagtgcccgactttgagtctattttattaaataagttttgacatgtacagGGCATGATGAACAACTGCTGGTTCAGAGTGAAAACCAATGTGTGCAGGCCCCACAAGGGTGAGATAGGTATAGTGTTTGAACACCCCACCCAACCAGGCA
|| | | || ||| | | | || | | || | | | | || | || | | | | | ||| | | ||||||||||||||||||||||||||| | ||||| | ||| | |||| |||| |||||||| ||||| || || ||||| || ||||| | || || ||||
gtgagttgccgctccatcgtgtttcccttcccgtggaaccatgcatgtcctcctctccacgactgtgttagcttaaatacacgcacgtgcgtctgttcctctacgcgcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGATCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCATGGTGTTCGAGCACCCGGCGCAGCCGGGCA
upper sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G428027_T01 (Zea mays), 3'ss of exon 3
-------------tagcaataaactattgcccgtgacttaaa---------atctaatcaaaatcttt-actaaagtgcccgactttgagtctattttattaaataagttttg-acatgtacagGGCATGATGAACAACTGCTGGTTCAGAGTGAAAACCAATGTGTGCAGGCCCCACAAGGGTGAGATAGGTATAGTGTTTGAACACCCCACCCAACCAGGCA
| | || || ||| ||| || || |||| || ||| || | | | | | | || | | ||||||||||||||||||||||||||| | ||||| ||| | |||| |||| |||||||| ||||| || | ||||| || ||||| || || || ||||
gtgagttaccgcttcatcgtgcttcctttccggtggcttcgccgtcggtccgtccgatgcttgtcttccacggctgtgttagattaaatgcacgtgtggcttgtccgttcctgcgcgcgcgcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGGTCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
upper sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G568636_T01 (Zea mays), 3'ss of exon 3
tagcaataaactattgcccgtgacttaaaatctaatcaaaatctttactaaagtgcccgactttgagtctattttattaaataagttttgacatg-tacagGGCATGATGAACAACTGCTGGTTCAGAGTGAAAACCAATGTGTGCAGGCCCCACAAGGGTGAGATAGGTATAGTGTTTGAACACCCCACCCAACCAGGCA
|| | || | |||| ||| | | ||| || | | | || || | || |||| | | ||| |||||| |||||||||||||||||||||| ||||| || |||||| | || |||||||| ||||| || | ||||| || ||||| || || || ||||
----------gtac-atatatatactagcacataatattaatactgaataa-gtttctgtttctgctcctgat--gatatataaatctgatgatggcacagGGGATGATGAACAACTGCTGGTTCAAGGTGAAGGTGAACGTGTGCCGTCCGCACAAGGGCGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCCGGCA
upper sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g03910.t01 (Vitis vinifera), 3'ss of exon 3
tagcaataaactattgcccgtgacttaaaatctaatcaaaatctttactaaagtgcccgactt--tgagtctattttattaaataagttttgacatgtacagGGCATGATGAACAACTGCTGGTTCAGAGTGAAAACCAATGTGTGCAGGCCCCACAAGGGTGAGATAGGTATAGTGTTTGAACACCCCACCCAACCAGGCA
| | | | | | | | | | | || ||| ||| | | || || | ||| || |||||| | || | | ||||| |||||||||||||||||||||||||| ||||| |||||||||| || |||| ||| ||||| || || || || || || || || | ||||| |
tcatagttg-caaacatgagaggcgtgcgtttatgacgtgat-tttcctataatttccattttgtcgtttctgattagggaaataataatggaattatgcagGGAATGATGAACAACTGCTGGTTCAGAGTAAAAACAAATGTGTGCAAGCGTCACAGGGGAGAGATTGGAATCGTATTCGAGCATCCAACTCTTCCAGGAA
upper sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S79_76V6.2 (Physcomitrella patens), 3'ss of exon 6
-------tagcaataaactattgcccgtgacttaaaatctaatcaaaatctttactaaagtgcccgactttgagtctattttattaaataagttttgacatg-tacagGGCATGATGAACAACTGCTGGTTCAGAGTGAAAACCAATGTGTGCAGGCCCCACAAGGGTGAGATAGGTATAGTGTTTGAACACCCCACCCAACCAGGCA
| || | ||| | | | | | || | | |||| | || | | || || | | | | | || || ||||||| ||||||||||||||||||||| | ||||| | | | || | || | | | || | | ||| || ||||| || || ||||| |
tgtttcgcatgcatccccagttgatcattccacatcccccaagcggattcttcattacaataatcgctgttctgaatgtcctc--------gccgtggtgtgctacagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGATCGGCATTACCAAGTCCGAAGACAACGGCATTCATCTGACGTTCGATCACCCGACTCAGCCAGGTAMapped 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|20813101|gb|BQ297579.1|BQ297579EST: GGGACGAGGCCCTCAACACCCAACCTGAAAAGCTCATTTGGAATGTTATG GGCATGATGAACAACTGCTGGTTCAGAGTGAAAACCAATGTGTGCAGGCCC
genomic: GGGACGAGGCCCTCAACACCCAACCTGAAAAGCTCATTTGGAATGTTATGgtacgttcct ... acatgtacagGGCATGATGAACAACTGCTGGTTCAGAGTGAAAACCAATGTGTGCAGGCCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactaaagtgcccgactttgagtctattttattaaataagttttgacatgtacagGGCATGATGAACAACTGCTGGTTCAGAGTGAAAACCAATGTGTGCAGGCCCCACAAGGGTGAGATAGGTATAGTGTTTGAACACCCCACCCAACCAGGCA
tttgagtctattttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagcaataaactattgcccgtgacttaaaatctaatcaaaatctttactaaagtgcccgactttgagtctattttattaaataagttttgacatgtacagGGCATGATGAACAACTGCTGGTTCAGAGTGAAAACCAATGTGTGCAGGCCCCACAAGGGTGAGATAGGTATAGTGTTTGAACACCCCACCCAACCAGGCA
- - - - - -tattgcc
- - - - - - - - - -gtgactt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cccgact