Sequence
atgc intronic sequence ATGC exonic sequence...gaatatctgatatctcaagttttgtattgtttcttagacaatgattttcttacattatttgtgagaagattatactgaaatgcttgctgttttcttgcagTCAAGCTGAACGCAAATCGCATGGTTGTTGGTACTCTCCGTGGCTTTGACCAGTTTATGAATTTAGTTGTTGACAACACTGTGGAAGTGAATGGCAATGA
Basic information
species | Glycine max |
transcript | GLYMA19G38130.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G38130.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g29740.1 (Oryza sativa), 3'ss of exon 2
----gaatatc--tgatatctcaagttttg-tattgtttcttagacaatgattttcttacattatttgtgagaagattatactgaaatgcttgctgttttcttgcagTCAAGCTGAACGCAAATCGCATGGTTGTTGGTACTCTCCGTGGCTTTGACCAGTTTATGAATTTAGTTGTTGACAACACTGTGGAAGTGAATGGCAATGA
|| | ||| || |||| |||||| || ||| ||| | ||| | || | | | |||| || |||| || ||||||||||||| ||||| || | |||||||||| |||||||| || || |||||||||||||| || || |||||||| || || || ||||| |||||
accttgatcttggtgaaatgatgggtttcaatattgtactttttacattgaggagtcctctttagtgtctagttg-taacactg------ttcaacttttttttcagTCAAGCTGAATGCAAACCGTGTAATTGTTGGTACGCTCCGTGGATTCGATCAGTTTATGAATTTGGTGGTGGACAACACGGTAGAGGTCAATGGAAATGA
upper sequence: GLYMA19G38130.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G11500.1 (Arabidopsis thaliana), 3'ss of exon 2
---gaatatctgatatctcaagttttgtattgtttcttagacaatgattttcttacattatttgtgagaagattatactgaaatgcttgctgttttct----tgcagTCAAGCTGAACGCAAATCGCATGGTTGTTGGTACTCTCCGTGGCTTTGACCAGTTTATGAATTTAGTTGTTGACAACACTGTGGAAGTGAATGGCAATGA
|||| | | || |||| ||| | | || | | | || | | | |||| || | | ||| |||| | || ||| ||||| || || || | ||||||||||| ||||||||||||||||| ||||| |||||| | ||||| || |||||||| ||||| ||||| ||||
ttagaat-tttactagactttgtttgttatcatgtttttg----taacttggtatggtca--agtgaagttcttgtctgcttttttttgttgttacccccaatgtagTTAAGCTTAATGCCAACAGAATGGTTGTTGGAACTCTCCGTGGCTTTGATCAGTTCATGAATCTTGTTGTGGATAACACTGTTGAAGTCAATGGTGATGA
upper sequence: GLYMA19G38130.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g03130.t01 (Vitis vinifera), 3'ss of exon 2
gaatatctgatatctcaagtttt--gtattgtttcttagacaatgattttcttacattatttgtgagaagattatactgaaatgcttgctgttttcttgcagTCAAGCTGAACGCAAATCGCATGGTTGTTGGTACTCTCCGTGGCTTTGACCAGTTTATGAATTTAGTTGTTGACAACACTGTGGAAGTGAATGGCAATGA
| || | | | | || ||||| || |||| | | || | | | | | | |||| | | | | ||| || | || | ||||||||||| |||| ||||| || ||||| ||||| ||||| ||||| ||||||||||| ||||| | || || ||||||||||||||||||||||| |||||
aagccccttgtgcatgatgcattaagtattagttgctagagactaatatatctgaaaaaact-tcagaacgtgaaatttaaactggtgat-ttatattgcagTCAAGTTGAATGCAAACCGGATGGTGGTTGGAACTCTTCGTGGGTTTGACCAGTTCATGAACCTGGTGGTGGACAACACTGTGGAAGTGAATGGAAATGAMapped 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|7042559|gb|AW472453.1|AW472453EST: AAGTACATGGATAAGAAGCTTCAGA TCAAGCTGAACGCAAATCGCATGGTTGTTGGTACTCTCCGTGGCTTTGACC
genomic: AAGTACATGGATAAGAAGCTTCAGAgtaagtctga ... tttcttgcagTCAAGCTGAACGCAAATCGCATGGTTGTTGGTACTCTCCGTGGCTTTGACC
EST:
gi|208259172|gb|GE055450.1|GE055450EST: CATGGATAAGAAGCTTCAGA TCAAGCTGAACGCAAATCGCATGGTTGTTGGTACTCTCCGTGGCTTTGACC
genomic: CATGGATAAGAAGCTTCAGAgtaagtctga ... tttcttgcagTCAAGCTGAACGCAAATCGCATGGTTGTTGGTACTCTCCGTGGCTTTGACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcttacattatttgtgagaagattatactgaaatgcttgctgttttcttgcagTCAAGCTGAACGCAAATCGCATGGTTGTTGGTACTCTCCGTGGCTTTGACCAGTTTATGAATTTAGTTGTTGACAACACTGTGGAAGTGAATGGCAATGA
ttcttac putative branch site (score: 2)
cttgctgttttctt putative PPT
tacattattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaatatctgatatctcaagttttgtattgtttcttagacaatgattttcttacattatttgtgagaagattatactgaaatgcttgctgttttcttgcagTCAAGCTGAACGCAAATCGCATGGTTGTTGGTACTCTCCGTGGCTTTGACCAGTTTATGAATTTAGTTGTTGACAACACTGTGGAAGTGAATGGCAATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgct