Sequence
atgc intronic sequence ATGC exonic sequenceGGGTTTAGCGACTCCAACTGCTGTTATGGTTGGGACCGGAGTTGGTGCATCTCAGGGTGTGCTCATCAAAGGAGGCCAAGCATTAGAGAGTGCACATAAGgtcagcatttgcatttcacatttgttagccacttgaattttggatttgcttagtctatgttggtgggcttaatattgaacggttaataaagttgcaagaa...
Basic information
species | Glycine max |
transcript | GLYMA01G42790.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G42790.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G144083_T01 (Zea mays), 5'ss of exon 3
GGGTTTAGCGACTCCAACTGCTGTTATGGTTGGGACCGGAGTTGGTGCATCTCAGGGTGTGCTCATCAAAGGAGGCCAAGCATTAGAGAGTGCACATAAGgtcagcatttgcatttcacatttgttagccacttgaattttggatttgcttagtctatgttggtgggcttaatattgaacggttaataaagttgcaagaa---------------------
|| | || || ||||||||||| ||||||| ||| ||||||||||| || || ||||| || ||||| || || ||||| | ||||||||||| ||||| | | | | ||| | | | |||| | ||| | || || || | || | | || | | | |
AGGGCTGGCTACCCCAACTGCTGTGATGGTTGCGACTGGAGTTGGTGCCTCACATGGTGTTCTGATCAAGGGTGGGCAAGCTCTGGAGAGTGCACAGAAGgtatgaaataatctcatctattgtgagggcgtgcaagtttttttcctttttaaaaaaggtcattgaa-ttgttcagaaatgctaaactatctcatatgccatggtacttggtacttcgtag
upper sequence: GLYMA01G42790.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv02s0025g03630.t01 (Vitis vinifera), 5'ss of exon 3
GGGTTTAGCGACTCCAACTGCTGTTATGGTTGGGACCGGAGTTGGTGCATCTCAGGGTGTGCTCATCAAAGGAGGCCAAGCATTAGAGAGTGCACATAAGgtcagcatttgcatttcacatttgttagccacttgaattttggatttgcttagtctatgttggtgggcttaatattgaacggttaa----taaagttgcaagaa
|| | || ||||| ||||| || |||||||| || || ||||| || ||||||||||| ||||||||||| || ||||||||||| ||||||||||||||||| | || | ||| || | || | | | | | ||||| || || ||| | | ||| |
AGGCCTTGCAACTCCTACTGCCGTCATGGTTGGTACTGGTGTTGGGGCCTCTCAGGGTGTCCTCATCAAAGGCGGTCAAGCATTAGAAAGTGCACATAAGgtcagtgtgtgaaactcatcttgcatgtttacgttttaaggaaaaacagacatcggagaataagattcttaagcttaaaaaactaaactttgaggtttta----
upper sequence: GLYMA01G42790.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv02s0025g03630.t01 (Vitis vinifera), 5'ss of exon 9
GGGTTTAGCGACTCCAACTGCTGTTATGGTTGGGACCGGAGTTGGTGCATCTCAGGGTGTGCTCATCAAAGGAGGCCAAGCATTAGAGAGTGCACATAAGgtcagcatttg-----catttcacatttgttagccactt---gaattttggat-ttgcttagtctatgttggtgggcttaatattgaacggttaataaagttgcaagaa
|| | || ||||| ||||||||||||||||| ||||| |||||||| |||||||| || ||||||||||| || ||||||||||| ||||||||||||||||| || || ||| | | || | | | ||| || ||| | | | || || || || | | | | ||| |
AGGCCTTGCAACTCCTACTGCTGTTATGGTTGGCACCGGTGTTGGTGCTTCTCAGGGAGTCCTCATCAAAGGCGGTCAAGCATTAGAAAGTGCACATAAGgtcagtatgtggtaatcatcttgcccttttcaaattttcaaggaagaacaaatcttggggaatgaagattcttgagcgaaaacctccatgttcaatcaca---------
upper sequence: GLYMA01G42790.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv02s0025g03640.t01 (Vitis vinifera), 5'ss of exon 2
GGGTTTAGCGACTCCAACTGCTGTTATGGTTGGGACCGGAGTTGGTGCATCTCAGGGTGTGCTCATCAAAGGAGGCCAAGCATTAGAGAGTGCACATAAGgtcagcatttgcatttcacatttgttagccacttgaattttggatttgcttagtctatgttggtgggcttaatattgaacggttaataaagtt-gcaagaa-----
||| | || ||||| ||||||||||||||||| || || ||||| || ||||||||||| ||||||||||| |||||||||||||| ||||||||||||||||| | || |||| ||| | || | ||| | | | || | | || |||| ||| | | ||||| | | |
GGGCCTTGCAACTCCTACTGCTGTTATGGTTGGTACTGGTGTTGGAGCTTCTCAGGGTGTCCTCATCAAAGGCGGCCAAGCATTAGAAAGTGCACATAAGgtcagtaagtggtattcat-cttgcc--cttctctactttctaa---agaaaagcaatcctaggggaattaagattcttgaactcaaaaagtccgtacttaaccac
upper sequence: GLYMA01G42790.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ17461 (Selaginella moellendorffii), 5'ss of exon 3
GGGTTTAGCGACTCCAACTGCTGTTATGGTTGGGACCGGAGTTGGTGCATCTCAGGGTGTGCTCATCAAAGGAGGCCAAGCATTAGAGAGTGCACATAAGgtcagcatttgca-------tttcacattt---gttagccacttgaattttggatttgcttagtctatgttggtgggcttaatattgaacggttaataaagttgcaagaa--------------------------------------------------------------------
||||| ||||| |||||||||||||| | || ||| |||||| | || ||||| || |||||||| ||| | ||||||||||||||||| ||||| ||| || |||| ||| | | ||| || | | | || | | ||| |||| || | | || | | | |
---CTTAGCTACTCCTACTGCTGTTATGGTCGCCACTGGAAAAGGTGCAGCCCAAGGTGTTCTAATCAAAGGTGGCAATGCATTAGAGAGTGCACAGAAGGTGgttattcacagacattctttcttctttcgagggaataactgaaaccacaggctag--taattcacattgctgggttttcttctttgtttttcctcttgcttcttctttttacgttttctttttctctctgcactttgcttgaaattaagactaatacttgtttgtgatgcttcag
upper sequence: GLYMA01G42790.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ28784 (Selaginella moellendorffii), 5'ss of exon 3
GGGTTTAGCGACTCCAACTGCTGTTATGGTTGGGACCGGAGTTGGTGCATCTCAGGGTGTGCTCATCAAAGGAGGCCAAGCATTAGAGAGTGCACATAAGgtcagcatttgca-------tttcacattt---gttagccacttgaattttggatttgcttagtctatgttggtgggcttaatattgaacggttaataaagttgcaagaa-------------------------------------------------------------------
||| ||||| ||||| |||||||||||||| | || ||| |||||| | || ||||| || |||||||| ||| | ||||||||||||||||| ||||| ||| || |||| ||| | | ||| || | | | || | | ||| |||| || | | ||| | | | |
GGGCTTAGCTACTCCTACTGCTGTTATGGTCGCCACTGGAAAAGGTGCAGCCCAAGGTGTTCTAATCAAAGGTGGCAATGCATTAGAGAGTGCACAGAAGgtggttattcacagacattctttcttctttcgagggaaaaactgaaaccacaggctag--taatacacattgctgggttttcttctttgttgttcctcttgcttcttctttttcgttttctttttctctctgcactttgcttgaaactaagactaatacttgtttgtgatgcttcagMapped 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|23729122|gb|BU762645.1|BU762645EST: CTCAGGGTGTGCTCATCAAAGGAGGCCAAGCATTAGAGAGTGCACATAAG GTGGACTGCATTGTTTTTGATAAGACGGGTACTCTCACTGTTGGGAAACCT
genomic: CTCAGGGTGTGCTCATCAAAGGAGGCCAAGCATTAGAGAGTGCACATAAGgtcagcattt ... tgtcttgtagGTGGACTGCATTGTTTTTGATAAGACGGGTACTCTCACTGTTGGGAAACCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGGTTTAGCGACTCCAACTGCTGTTATGGTTGGGACCGGAGTTGGTGCATCTCAGGGTGTGCTCATCAAAGGAGGCCAAGCATTAGAGAGTGCACATAAGgtcagcatttgcatttcacatttgttagccacttgaattttggatttgcttagtctatgttggtgggcttaatattgaacggttaataaagttgcaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttggtgg