Sequence
atgc intronic sequence ATGC exonic sequence...ccaattctagaaatttcaatttcaatgttaatttttattgtgattattattttttatagatcttttgtgcataaagtgataatggtgacaaatgttgcagAGAGATTATGCATGCCATGTGGAAGCCCCAAAAGTTCAAGTACATCTACTTGCTGGCCACTTTGTACGTTTTCACGCTAACGATTCCGTCCGCCGTCGCC
Basic information
species | Glycine max |
transcript | GLYMA03G09100.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G09100.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0007g02030.t01 (Vitis vinifera), 3'ss of exon 6
-ccaattctagaaatttcaatttcaatgttaatttttattgtgattattattttttatagatcttttgtgcataaagtgataatggtgacaaatgttgcagAGAGATTATGCATGCCATGTGGAAGCCCCAAAAGTTCAAGTACATCTACTTGCTGGCCACTTTGTACGTTTTCACGCTAACGATTCCGTCCGCCGTCGCC
||| || | | || | | || | | ||| | | | | | || || || || | || | | ||||| ||| || || ||||| ||||||||||| ||||| || ||||||||||| ||||| ||||||| | ||||||||||| ||||| |||| || || ||||
aagaatgaagagaactagtgtaataaattcatttctagtcttgagtttcggataagaaaaatgggttctg-atccgtgaagggtgacggaatatgtttcagGGAAATCATGCACGCCATGTGGAAACCCCAGAAATTCAAGTACATATACTTAATGGCCACACTCTACGTTTTCACTCTAACACTTCCCTCAGCTTCCGCC
upper sequence: GLYMA03G09100.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ34222 (Selaginella moellendorffii), 3'ss of exon 5
ccaattctagaaatttcaatttcaatgttaatttttattgtgattattattttt-tatagatcttttgtgcataaagtgataatggtgacaaatgttgcagAGAGATTATGCATGCCATGTGGAAGCCCCAAAAGTTCAAGTACATCTACTTGCTGGCCACTTTGTACGTTTTCACGCTAACGATTCCGTCCGCCGTCGCC
|| | ||| | | | || || || |||| | | |||| | |||| | | ||| ||||| ||||| || ||||||||||||||||||||||||| |||| | | || || | ||||| ||||| | || | ||||||||| ||
--------------------------gtaagctttcgcttctttcgctgttcttgcatggatcgatag-gcatcttctcataa--actttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
upper sequence: GLYMA03G09100.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
ccaattctagaaatttcaatttcaatgttaatttttattgtgattattattttttatag--atcttttgtgcataaagtgataatggtgacaaatgttgcagAGAGATTATGCATGCCATGTGGAAGCCCCAAAAGTTCAAGTACATCTACTTGCTGGCCACTTTGTACGTTTTCACGCTAACGATTCCGTCCGCCGTCGCC
|| || ||| | || || ||| || | | | | ||||||| | |||||| | | | ||| ||||| ||||| || ||||||||||||||||||||||||| |||| | | || || | ||||| ||||| | || | ||||||||| ||
--------gtaagctttcgcttctttcgctgttcttgcatggatcgataggctatgttgtcatcttttct-cataaact----------ttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCAMapped 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|105632824|gb|DW246546.1|DW246546EST: ACTGGAGCCACTAACATACTCTACACGTTTGGAGGACATGCTGTGACTGT AGAGATTATGCATGCCATGTGGAAGCCCCAAAAGTTCAAGT
genomic: ACTGGAGCCACTAACATACTCTACACGTTTGGAGGACATGCTGTGACTGTgtgagttcac ... aatgttgcagAGAGATTATGCATGCCATGTGGAAGCCCCAAAAGTTCAAGT
EST:
gi|209726838|gb|BW658346.1|BW658346EST: ACTGGAGCCACTAACATACTCTACACGTTTGGAGGACATGCTGTGACTGT AGAGATTATGCATGCCATGTGGAAGCCCCAAA-GTTCAAGTACATCTACTT
genomic: ACTGGAGCCACTAACATACTCTACACGTTTGGAGGACATGCTGTGACTGTgtgagttcac ... aatgttgcagAGAGATTATGCATGCCATGTGGAAGCCCCAAAAGTTCAAGTACATCTACTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attattttttatagatcttttgtgcataaagtgataatggtgacaaatgttgcagAGAGATTATGCATGCCATGTGGAAGCCCCAAAAGTTCAAGTACATCTACTTGCTGGCCACTTTGTACGTTTTCACGCTAACGATTCCGTCCGCCGTCGCC
tttttatagatctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccaattctagaaatttcaatttcaatgttaatttttattgtgattattattttttatagatcttttgtgcataaagtgataatggtgacaaatgttgcagAGAGATTATGCATGCCATGTGGAAGCCCCAAAAGTTCAAGTACATCTACTTGCTGGCCACTTTGTACGTTTTCACGCTAACGATTCCGTCCGCCGTCGCC
- - - - - - - - - - - caatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgac