Sequence
atgc intronic sequence ATGC exonic sequence...gttctggtttgttgttgagatcttgatgtggcaaataagcaatgtcctgcagtgaaattgcaaagcatctttcacttccaccagttaagctccactgcagCATGCTTGCTGAAGATGCTATCAAAGCGGCCGTTAAAGACTATGAAGCTAAGCGTGCTAAGGCAACTGCTAGCGGAGAGGCAGCAACAGAAGAGAAGCCT
Basic information
species | Glycine max |
transcript | GLYMA17G09670.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G09670.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S76_212V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------gttctggtttgttgttgag------atcttgatgtggcaaataagc-aatgtcctgcagtgaaattgcaaagcatctttcacttccaccagttaagctccactgcagCATGCTTGCTGAAGATGCTATCAAAGCGGCCGTTAAAGACTATGAAGCTAAGCGTGCTAAGGCAACTGCTAGCGGAGAGGCAGCAACAGAAGAGAAGCCT
| | | |||| | || | | ||| | || | || | ||||||||| || || ||||| || || || ||||| || ||| | |||||||||||||||||||||||||||||||||||||| || || ||||| | | |||
attggttggcatggattaccgcagtgtgtcttaggccctcagaacaaatgtgttcctaaggatataagttaaatggtggggatgtgtgaactttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCGGTGAAGGACTACAAGTCCAAG------------------------------------------------
upper sequence: GLYMA17G09670.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S39_352V6.2 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------gttctggtttgttgttgagatcttgatgtggcaaataagcaatgtcct---gcagtgaaattgcaaagcatctttcacttccaccagttaagctccactgcagCATGCTTGCTGAAGATGCTATCAAAGCGGCCGTTAAAGACTATGAAGCTAAGCGTGCTAAGGCAACTGCTAGCGGAGAGGCAGCAACAGAAGAGAAGCCT
||| | || | |||| || | | | | | | ||||||| ||||| || ||| | || | ||||| || ||| | |||||||||||||||||||| |||||||| |||||||| || || ||||| | |||||
gtgtacaaggcattatgtgtgagtactttatgggtgttgacctattttccattatgcttgaaagattaaagcatgtggtgtgggtattttttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAGGATGCTATTAAAGCGGCTGTGAAGGACTACAAGGCTAAA------------------------------------------------
upper sequence: GLYMA17G09670.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ10697 (Selaginella moellendorffii), 3'ss of exon 2
--gttctggtttgttgttgagatcttgatgtggcaaa----taagcaatgtcct----gcagtgaaattgcaaagcatctttcacttccaccagttaagctccactgcagCATGCTTGCTGAAGATGCTATCAAAGCGGCCGTTAAAGACTATGAAGCTAAGCGTGCTAAGGCAACTGCTAGCGGAGAGGCAGCAACAGAAGAGAAGCCT
| || ||| ||| | | ||| || | | | || | ||||||| || || |||||||| || || || ||||| ||||||||||||||||||||||| || ||||| |||||||| || | ||||| || || || |||
gtaacttttcttcttgagaggatttctccgaggctaagctctctcctctttcttcttcgcagTGACATCGCCAAGCATCTGTCGCTGCCGCCAGTGAAGCTCCACTGCAGCATGCTTGCCGAGGATGCGATCAAAGCCGCGATCAAAGATTACGACGCGAAG------------------------------------------------
upper sequence: GLYMA17G09670.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ35746 (Selaginella moellendorffii), 3'ss of exon 2
--gttctggtttgttgttgagatcttgatgtggcaaa---taagcaatgtcct-----gcagtgaaattgcaaagcatctttcacttccaccagttaagctccactgcagCATGCTTGCTGAAGATGCTATCAAAGCGGCCGTTAAAGACTATGAAGCTAAGCGTGCTAAGGCAACTGCTAGCGGAGAGGCAGCAACAGAAGAGAAGCCT
| | || ||| ||| || | ||| || | | | || ||||||| || || |||||||| || || || ||||| ||||||||||||||||||||||| || ||||| |||||||| || | ||||| || || || |||
gtaatttttcttcttgagaggatttttccgaggctaagctcattcctctttcttcttcgcagTGACATCGCCAAGCATCTGTCGCTACCGCCAGTGAAGCTCCACTGCAGCATGCTTGCCGAGGATGCGATCAAAGCCGCGATCAAAGATTACGACGCCAAG------------------------------------------------Mapped 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|58022474|gb|CX709215.1|CX709215EST: GAGTGGGTGAAGGGAAGGCAAATGGAGGAAGTTCTGACTATAAAAAATAC CATGCTTGCTGAAGATGCTATCAAAGCGGCCGTTAAAGACTATGAAGCTAA
genomic: GAGTGGGTGAAGGGAAGGCAAATGGAGGAAGTTCTGACTATAAAAAATACgtaagtatac ... tccactgcagCATGCTTGCTGAAGATGCTATCAAAGCGGCCGTTAAAGACTATGAAGCTAA
EST:
gi|58022153|gb|CX708894.1|CX708894EST: GAGTGGGTGAAGGGAAGGCAAATGGAGGAAGTTCTGACTATAAAAAATAC CATGCTTGCTGAAGATGCTATCAAAGCGGCCGTTAAAGACTATGAAGCTAA
genomic: GAGTGGGTGAAGGGAAGGCAAATGGAGGAAGTTCTGACTATAAAAAATACgtaagtatac ... tccactgcagCATGCTTGCTGAAGATGCTATCAAAGCGGCCGTTAAAGACTATGAAGCTAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgcagtgaaattgcaaagcatctttcacttccaccagttaagctccactgcagCATGCTTGCTGAAGATGCTATCAAAGCGGCCGTTAAAGACTATGAAGCTAAGCGTGCTAAGGCAACTGCTAGCGGAGAGGCAGCAACAGAAGAGAAGCCT
ctccact CT-rich tract
tgaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttctggtttgttgttgagatcttgatgtggcaaataagcaatgtcctgcagtgaaattgcaaagcatctttcacttccaccagttaagctccactgcagCATGCTTGCTGAAGATGCTATCAAAGCGGCCGTTAAAGACTATGAAGCTAAGCGTGCTAAGGCAACTGCTAGCGGAGAGGCAGCAACAGAAGAGAAGCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- tctggtt
- - - - - gttgttg
- - - - - - - - - - - - gatgtgg
- - - - - - - - - - - - - - - - - - -agcaatg
- - - - - - - - - - - - - - - - - - - - - - tcctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaagca