Sequence
atgc intronic sequence ATGC exonic sequencegtatgagcttagatgattttcatatgcagtttgtagttaagaaaggttcacattgatgcttccatatgtttgttatctgcagATATATTAAGGAAAGAAAAGAAAAGGATCCAGAGGTTGAGATTGAAGTAGCAACCAAGTTTGCTGCACTGCCGTGGAGATTTGGCCGTCAAAGTGTTCTC
Basic information
species | Glycine max |
transcript | GLYMA18G14510.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G14510.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g04990.1 (Oryza sativa), 3'ss of exon 3
-----------------gtatgagcttagatgattttcatatgcagtttgtagttaagaaag----gttcacattgatgcttccatatgtttgt------tatctgcagATATATTAAGGAAAGAAAAGAAAAGGATCCAGAGGTTGAGATTGAAGTAGCAACCAAGTTTGCTGCACTGCCGTGGAGATTTGGCCGTCAAAGTGTTCTC---
|| | || |||| || | ||| | || ||||| | || || | | | | |||| | | ||| | || |||||||| | || || || | || |||| ||| || ||||| |||||||||||||| || |||||||||||||| |||||||||
gtatgccacgttttgctgttcagcactccattttttttat-tattttttatttttgcgaaagtcacatgtgcagcaatagtcacctgttgttgtctctcttgccgccagTTTCATCAAGGAAAGGCAGGAGAAAGAAC---AGATTGATGTTGCCGTCGCAACAAAGTTTGCTGCACTTCCATGGAGATTTGGCCGAGGAAGTGTTCTTTCC
upper sequence: GLYMA18G14510.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G06690.1 (Arabidopsis thaliana), 3'ss of exon 3
gta-tgagcttagatgattttca----tatgcagtttgtagttaagaaaggttcacattgatgcttccatatgtttgttatctgcagATATATTAAGGAAAGAAAAGAAAAGGATCCAGAGGTTGAGATTGAAGTAGCAACCAAGTTTGCTGCACTGCCGTGGAGATTTGGCCGTCAAAGTGTTCTC
||| | | || || | | | | ||| | | | | ||| |||| | || || ||||| || || |||||||| | |||| | | |||| || || |||||||||||||||||| |||| ||| ||||||| ||| |||||||| ||
gtaatttgtttcgaaaacatataacagtgtgccacactatcctcatatatattcctcttgactgtcattggtgagattttcgaacagATTCATCCGTGAGAGAAAAGAGAGATATCCCGGAGCTGAGGTTTCGGTTGCAACCAAGTTTGCTGCATTGCCATGGCGATTTGGTCGTGAAAGTGTTGTC
upper sequence: GLYMA18G14510.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0028g01100.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------gtatgagcttagatgattttca--tatgcag--tttgtagttaagaaaggttcacattgatgcttccatatgtttgttat-ctgcagATATATTAAGGAAAGAAAAGAAAAGGATCCAGAGGTTGAGATTGAAGTAGCAACCAAGTTTGCTGCACTGCCGTGGAGATTTGGCCGTCAAAGTGTTCTC
| || | | || | | | ||| ||| | |||| | ||||| | || | | | | || ||| | | || | ||||| ||||||||||||||| ||||||| || ||| ||| || |||||||||||||| || | || ||||| ||||| ||||| ||||| ||
gtaagttgtgagaatttgataatggcttgcatttcatgtttcccaaaactcacagaatccagaagtttccagcatttatttttaatcatggttc----taattatccaacttattggttttgttaaagGTTCATTAAAGAAAGAAAAGAAAAGAATCCAGAAGTGGAGGTTGCTGTTGCAACCAAGTTTGCAGCTTTACCATGGAGGTTTGGACGTCAGAGTGTAATC
upper sequence: GLYMA18G14510.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ32160 (Selaginella moellendorffii), 3'ss of exon 4
gtatgagcttagatgattttcatatgcagtttgtagttaagaaaggttcacattgatgcttccatatgtttgttatctgcagATATATTAAGGAAAGAAAAGAAAAGGATCCAGAGGTTGAGATTGAAGTAGCAACCAAGTTTGCTGCACTGCCGTGGAGATTTGGCCGTCAAAGTGTTCTC---
||| ||| | | ||| | | || | | |||| | ||| ||||| | ||| || | || | | | |||||| ||| ||||| ||||||||||||||||| ||||| |||||||| || ||| ||
--------------------------------gtaaacaagcttgtcttctatttttcaagttttcctctttcttcccgcagGTTTATCAAGGAGATCAAACAAGAAGAGC---AATCTAAGATTGTAGTGGCAACGAAGTTTGCTGCACTGCCATGGAGGTTTGGCCGAGGGAGCGTTGTCAAA
upper sequence: GLYMA18G14510.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ16831 (Selaginella moellendorffii), 3'ss of exon 5
gtatgagcttagatgattttcatatgcagtttgtagttaagaaaggttcacattgatgcttccatatgtttgttatctgcagATATATTAAGGAAAGAAAAGAAAAGGATCCAGAGGTTGAGATTGAAGTAGCAACCAAGTTTGCTGCACTGCCGTGGAGATTTGGCCGTCAAAGTGTTCTC---
||| ||| | | ||| | | || | | |||| | ||| ||||| | ||| || | || | | | |||||| ||| ||||| ||||||||||||||||| ||||| |||||||| || ||| ||
--------------------------------gtaaacaagcttgtcttctatttttcaagttttcctctttcttcccgcagGTTTATCAAGGAGATCAAACAAGAAGA---ACAATCTAAGATTGTAGTGGCAACGAAGTTTGCTGCACTGCCATGGAGGTTTGGCCGAGGGAGCGTTGTCAAAMapped 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|12690416|gb|BG156752.1|BG156752EST: CTTGCTTTAGGAGCCATAAATTCTGAGGTTCTTCTTGGAAG ATATATTAAGGAAAGAAAAGAAAAGGATCCAGAGGTTGAGATTGAAGTAGC
genomic: CTTGCTTTAGGAGCCATAAATTCTGAGGTTCTTCTTGGAAGgtatgagctt ... ttatctgcagATATATTAAGGAAAGAAAAGAAAAGGATCCAGAGGTTGAGATTGAAGTAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtttgtagttaagaaaggttcacattgatgcttccatatgtttgttatctgcagATATATTAAGGAAAGAAAAGAAAAGGATCCAGAGGTTGAGATTGAAGTAGCAACCAAGTTTGCTGCACTGCCGTGGAGATTTGGCCGTCAAAGTGTTCTC
cattgat putative branch site (score: 4)
ttaagaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgagcttagatgattttcatatgcagtttgtagttaagaaaggttcacattgatgcttccatatgtttgttatctgcagATATATTAAGGAAAGAAAAGAAAAGGATCCAGAGGTTGAGATTGAAGTAGCAACCAAGTTTGCTGCACTGCCGTGGAGATTTGGCCGTCAAAGTGTTCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT