Sequence
atgc intronic sequence ATGC exonic sequenceGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtctacaatggttagttacatccattcttgaatatgttatatagttatggattcatctcaacctgtgctcatatagggtgcacggttcacatttgt...
Basic information
species | Glycine max |
transcript | GLYMA06G06310.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G06310.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os02g05630.1 (Oryza sativa), 5'ss of exon 6
GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtctacaatggttag-ttacatccattcttgaatatgttatatagttatggattcatctcaacctgtgctcatatagggtgcacggttcacatttgt
| || ||| | ||||| |||||||||||||||||||| || |||||||||| || ||||||||||||| |||||||||||||| || |||| || || | | ||| | ||| || || | | ||| | | || ||| | | | |||| | | | | |
GGACGTGGCGTGTTGGTGGTGTTCTTGCTGTTTCTCGAGCATTTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGgtttgacttaatttgtttgcttagctctcaactaaagccttctatctgcaaaataatattcatcatcgtaattggcattcccatgcatgttactctaaag-
upper sequence: GLYMA06G06310.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os06g48300.1 (Oryza sativa), 5'ss of exon 6
GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgt------atgtctacaatggttagttacat--------ccattcttgaatatgttatatagttatggattc------atctcaacctgtgctcatatagggt---gcacggttcacatttgt-----------------------------------
|||| ||| | || || |||||||||||||| ||||| || |||||||| | |||||||||||| ||||| |||||||||||||| || |||| | ||| | | | | | ||| | || | || | ||||| || | || ||| | | ||||| || | || ||| | | |
GAACATGGCGCGTGGGTGGTGTTCTTGCTGTCTCTCGAGCATTTGGTGACAAACTCCTGAAGCAATATGTGGTTGCTGATCCAGAGATCAAGgtcctcaagtttcttccaatctcaaattcataattcatgcagctcataaagaaagtatatgcatagaggccatgaacgatttcaggatacgaccatattacgttatgtactgttgcaaatcgaaattcgacatttatctgcttatttgatctgtacag
upper sequence: GLYMA06G06310.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os04g56450.2 (Oryza sativa), 5'ss of exon 6
GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtctacaatggttagttacatccattcttgaatatgttatatagttatggattcatctcaacctgtgctcat-atag--ggtgcacggttcacatt-tgt
|||| ||| | ||||| ||||| |||||||||||||| || |||||||| | |||| | ||||||||||| |||| ||||| || |||| |||||| | | || | || || || || | | | || | || ||| | | | | ||| | || |||| ||| || || ||
GAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGGgtatg-caatcctgaccaatttaatgt-ttgttatgtctact-tacctctcaaaatgcatatgtaggtatcaccatgacagtaggtgaacgtttggaatcatg-
upper sequence: GLYMA06G06310.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM5G829894_T03 (Zea mays), 5'ss of exon 1
--------GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtctacaatggttagttacatccattcttgaatatgttatatagttat--ggattcatctcaacctgtgctcatatagggtgcacggttcacatttgt---------------------------------------------------------------------------------------------------
| || ||| |||| || |||||||||||||| ||||| || |||||||||| |||| |||||||||||||||| ||||| || ||||| |||| |||| ||| | ||| | | | || |||||| | || ||| || | |||| | | | | | | | ||||
ATTTGTAGGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAGgtttgtc----atg--cacttatgttttattacggattgtcgggatagtttttcagacctatcatggtttgagggaatatggtggg---gttgtaaacttgtaataagtgcctaaaaatggggattccatcatttagcaatgtcatacatcacccacaccccctgtagccatctgaaaacgatttttgctgttacaatcag
upper sequence: GLYMA06G06310.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM5G829894_T02 (Zea mays), 5'ss of exon 4
GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtctacaatggttagttacatccattcttgaatatgttatatagttat--ggattcatctcaacctgtgctcatatagggtgcacggttcacatttgt---------------------------------------------------------------------------------------------------
| || ||| |||| || |||||||||||||| ||||| || |||||||||| |||| |||||||||||||||| ||||| || ||||| |||| |||| ||| | ||| | | | || |||||| | || ||| || | |||| | | | | | | | ||||
GGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAGgtttgtc----atg--cacttatgttttattacggattgtcgggatagtttttcagacctatcatggtttgagggaatatggtggg---gttgtaaacttgtaataagtgcctaaaaatggggattccatcatttagcaatgtcatacatcacccacaccccctgtagccatctgaaaacgatttttgctgttacaatcag
upper sequence: GLYMA06G06310.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 6
GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtc---tacaatggttagttacatccatt-cttgaatatgttatatagttatggattcatctca--acctgtgct-catatagggtgcacggttcacatttgt--------------------------------------------------------------------------------
| || |||||||| || || ||||| ||||| ||||| || |||||||||| |||| |||||| ||||||||||||||| || ||||| |||| |||| | | ||| | || ||| | || |||| || | | || | | | | | | || | | | | | | | | | | |
GGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatgcatttttgtttttactatggattgcctggatattttttccaaacatatcatggtttgaggaaatatggtgcgtttgtaataaatgcctaaaaacggggatcccatcataagcaatgtcatacatcactcccaacccccctgtagccatctgaaaacggcttttgctattacaatcag
upper sequence: GLYMA06G06310.1 (Glycine max), 5'ss of exon 6
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 5'ss of exon 7
GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtat--gtctacaatggttagttacatccat-tcttgaatatgttatatagttatggattcatctcaacctgtgctcatatagggtgc--acggttcacatttgt
|||| |||||||||||||| |||||||||||||||||||| ||||| ||||| | ||||||||||||||||||||||||| || || ||||||| | | | | | || | || || ||| | | ||||| | || | ||| | | || || | | ||| | |
GAACATGGAGAGTTGGAGGAGTTCTTGCTGTTTCTCGTGCATTTGGCGATAGGTTGTTGAAGCAGTATGTTGTTGCTGATCCGGAGATACAGgtattgactttttgccaaaatctcctcctatatattaaaaatgccactttgttattaa--caattgaacata-acctgcattggatttcaatagttagctact--
upper sequence: GLYMA06G06310.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 5'ss of exon 7
GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtctacaatggttagttacatccattcttgaatatgttatatagtta-tggattcatctcaacctgtgctcatatagggtgcacggttcacatttgt
|||||||||| ||||| ||||||||||||||||||||||| ||||||||||||||| ||||||||||||||||||||||||||||||| ||||| || || | ||| | | | |||| || | | | || | ||| || || | |||| | |
GAACTTGGAGGGTTGGGGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCTTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAGgtctggctctgagagttgatagtaaagctagttga-cataatttgcatctagcgaattttatgcagttaaaatctattccaagggcactcctaggcagaat
upper sequence: GLYMA06G06310.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S225_37V6.1 (Physcomitrella patens), 5'ss of exon 6
GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtctacaatggttagtt-------acatccatt--cttgaatatgttatatagttatggattcat-ctcaacctgtgctcatatagggtgcacggttcacatttgt--
| |||||| | || || || ||||||||||| ||||| || ||||||||| | || ||||| | ||||||||||| || |||||||||||||| | | | | ||| ||| ||||||| | | || | ||||| || || || | | | | | | | | | ||
GTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATCGGCTGCTGAAAAAATATGTTGTTGCCGAACCAGAAATTCAGgttagctcatcgtttctgccctcttagcacaataattaacttgaatttcagagttattagtggatgtatgctgaagatatctttgcttctgatttttttgtttcctgtgcag
upper sequence: GLYMA06G06310.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S174_123V6.1 (Physcomitrella patens), 5'ss of exon 6
GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtcta-----caatggttagt-------tacatccattc-ttgaatatgtta---tatagttatggat-----tcatctcaacctgtg----ctcatatagggtgcacggttcacatttgt------
| |||||| | || || || |||||||| || ||||| ||||||||||| || | || || ||||||||||||| || ||||||||||||||||| ||| | || | | |||| | ||| |||| |||| | ||| |||| | ||||| | || | | || | | | ||| || |||
GCACTTGGCGTGTAGGTGGCGTTCTTGCAGTCTCTCGGGCGTTTGGTGACCGATTGCTCAAAAAGTATGTTGTTGCGGAACCAGAAATTCAGgtatggctaactttcgttgactggcgtcttcatacagcaattgattgacccagttagggtgaagtagtggaaatgtgttatctctgattctggatttttacattgattttattgtttactggtgtgctcagMapped 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|14260019|gb|BG882927.1|BG882927EST: TTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG GAAGAAAAAATTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGG
genomic: TTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtctac ... cattttgcagGAAGAAAAAATTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtctacaatggttagttacatccattcttgaatatgttatatagttatggattcatctcaacctgtgctcatatagggtgcacggttcacatttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT