Sequence
atgc intronic sequence ATGC exonic sequencegtaagcccattttaaattaaataatgatttctcgtcaagattcaaactaagtatgacaatgatgctctattcagGGTCCGCATGCACTATGGGCATCCTGATGTTTTTGATAGAATATTCCACATAACCCGTGGTGGTATCAGCAAGGCTTCCCGTGTTATCAACATTAGTGAA
Basic information
species | Glycine max |
transcript | GLYMA20G38860.1 |
intron # | 40 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 40
lower sequence: LOC_Os03g02756.1 (Oryza sativa), 3'ss of exon 4
gtaagcccattttaaattaaataatgatttctcgtcaaga-----ttcaaactaagta-tgacaa----tgatgctctatt-cagGGTCCGCATGCACTATGGGCATCCTGATGTTTTTGATAGAATATTCCACATAACCCGTGGTGGTATCAGCAAGGCTTCCCGTGTTATCAACATTAGTGAA
||||| | ||||| || | ||| || ||| || ||||| || || || ||| || ||| || ||| || | ||||| ||||| ||||| ||||||||||||||||| || || ||||| | ||||| || || ||||| |||||||| ||||| || |||||
gtaagtgc-ttttacataatatatattttctatttcatgagtcatttcaagttacatactgtcaacatttggaattcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAG
upper sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 40
lower sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 3
gtaagcccattttaaattaaataatg---atttctcgtcaagat----tcaaactaagtatgacaa-----tgatgctctattc-----agGGTCCGCATGCACTATGGGCATCCTGATGTTTTTGATAGAATATTCCACATAACCCGTGGTGGTATCAGCAAGGCTTCCCGTGTTATCAACATTAGTGAA
||||| | ||||| || || | |||| | | | ||| | ||| | || | | ||| | | | || || | ||||||||||| ||||| ||||||||||||||||| || || ||||| | ||||| || || ||||| || || ||||| || |||||
gtaagtgc-ttttacatagtatgttttctgtttcacatgaggatcagctaaaattgtgtgtagttaatacatgaaaccttttcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG
upper sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 40
lower sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 37
gtaagcccattttaaattaaataatgatttctcgtcaa-gattcaaactaag----------tatgacaatgatgctctattc-agGGTCCGCATGCACTATGGGCATCCTGATGTTTTTGATAGAATATTCCACATAACCCGTGGTGGTATCAGCAAGGCTTCCCGTGTTATCAACATTAGTGAA
||||| | | ||| ||| | || | ||| || | | |||| || ||| | | | || |||| ||| |||||||||| ||||| ||||| ||||| ||||| ||| |||| || || || |||||||||||||||||||| || || || ||||| |||||||||
gtaagtt-actaccaat--aatttttatcttccgtgaacaacttgaactcagatggaatccttattctattatttctgaattctagGATCCGCATGCATTATGGTCATCCAGATGTCTTTGACAGAGTATTTCATATTACACGTGGTGGTATCAGCAAGGCCTCTCGGGTCATCAATATTAGTGAA
upper sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 40
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 35
gtaagcccatttta--aattaaataat------gatttctcgtca----agattcaaactaagtatgacaatgatgctctat-----tcagGGTCCGCATGCACTATGGGCATCCTGATGTTTTTGATAGAATATTCCACATAACCCGTGGTGGTATCAGCAAGGCTTCCCGTGTTATCAACATTAGTGAA
||||| ||||| | || || ||| ||| || ||| | ||| ||| | | || | || |||||| || ||||| ||||| ||||| ||||||||||||||| | ||||| ||||| || ||||||||||||||||| || || ||||||||||||||||||
gtaagttcatttaattaagcaagcaatttatttgatgtcatatcattttaaatttgggataactggagctgaaatctttaataatggccagGGTTCGTATGCATTATGGCCATCCAGATGTTTTTGATAGAGTTTTCCATATAACACGAGGTGGTATCAGCAAGGCCTCTCGAGTTATCAACATTAGTGAA
upper sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 40
lower sequence: PP1S67_234V6.1 (Physcomitrella patens), 3'ss of exon 39
-------------gtaagcc--cattttaaattaaataatgatttctc------gtcaagattcaaa---ctaagtatgacaatgatgctc--tattcagGGTCCGCATGCACTATGGGCATCCTGATGTTTTTGATAGAATATTCCACATAACCCGTGGTGGTATCAGCAAGGCTTCCCGTGTTATCAACATTAGTGAA
|||| | | || ||| | || ||| | | |||| || | || ||||| | | | |||||| | ||||| ||||| ||||| |||||||||||| | |||||||| ||||| | || ||||||||||| |||| || || | ||||||
aattatatgtgctgtaaatcgttagttctaatctagtatgactttgccttaggtgccaaggtttcgatgacttcgtatggttgctacatatgatgtgcagGGTGAGGATGCATTATGGTCATCCCGATGTTTTTGATCGTATATTCCATATAACAAGGGGAGGTATCAGCAAACCTTCAAAACAAATTAATCTCAGTGAA
upper sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 40
lower sequence: PP1S40_186V6.2 (Physcomitrella patens), 3'ss of exon 22
--------------------------------------------------------------------------------------------------------gtaagcccattttaaattaaataatgatttctcgtcaagattcaaa---ctaagtatgacaa--tgatgctctattcagGGTCCGCATGCACTATGGGCATCCTGATGTTTTTGATAGAATATTCCACATAACCCGTGGTGGTATCAGCAAGGCTTCCCGTGTTATCAACATTAGTGAA
||| | || ||| | | || |||| || | || |||||| | | || |||||| | ||||||||||| ||||| |||||||| ||| | |||||||||||||| | || ||||||||||| |||| | ||||| | ||| ||
gtgagttttctggcaagttctgactattttctgcatatttgttagattgtatatttctttcatatcttcaacctcttaaggataagaaaaagttgtaggggaactcaagaactttgaaaagctttcttgcacatgtcatcaaagtttcgatgactttgtatgattaattcgcatgctcggcagGGTAAGAATGCACTATGGTCATCCCGATGTTTTCGATCGGATATTCCACATAACAAGGGGAGGTATCAGCAAATCTTCAAAAGAGATCAATCTGAGTAAAMapped 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|193510265|gb|FK469815.1|FK469815EST: GAAACTAGTTTTGTGACTTTGGGGCAGCGAGTTTTAGCAAATCCATTGAA GGTCCGCATGCACTATGGGCATCCTGATGTTTTTGATAGAATATTCCACAT
genomic: GAAACTAGTTTTGTGACTTTGGGGCAGCGAGTTTTAGCAAATCCATTGAAgtaagcccat ... ctctattcagGGTCCGCATGCACTATGGGCATCCTGATGTTTTTGATAGAATATTCCACAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aataatgatttctcgtcaagattcaaactaagtatgacaatgatgctctattcagGGTCCGCATGCACTATGGGCATCCTGATGTTTTTGATAGAATATTCCACATAACCCGTGGTGGTATCAGCAAGGCTTCCCGTGTTATCAACATTAGTGAA
ctctattc CT-rich tract
attcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcccattttaaattaaataatgatttctcgtcaagattcaaactaagtatgacaatgatgctctattcagGGTCCGCATGCACTATGGGCATCCTGATGTTTTTGATAGAATATTCCACATAACCCGTGGTGGTATCAGCAAGGCTTCCCGTGTTATCAACATTAGTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG