Sequence
atgc intronic sequence ATGC exonic sequenceGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGAgtaaattctcctttgtttttatctttgttacatgttttgaagctttttgtgaattgttttttgtgaaaaaagttgggttgctattgtgggtatgtggtaa...
Basic information
species | Glycine max |
transcript | GLYMA16G03940.2 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G03940.2 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os10g31000.1 (Oryza sativa), 5'ss of exon 2
GATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGAgtaaattctcctttgt---ttttatctttgttacatgttttgaagctttttg--tgaattgttttttgtgaaaaaagttgggttgctattgtgggtatgtggtaa
||||||||| |||||||||||||||||| | || ||||| ||||| ||||| | ||| | |||| || || | ||| |||| || | | || |||||| | | | || || || | | | ||| || | | | | |
GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAAgtacgatcgcgcacgcaaattccgattttgtttttcctcctcctggttcctggcctgatgatccgcgtttcttgttttccggtctctgatctagatgtag-----
upper sequence: GLYMA16G03940.2 (Glycine max), 5'ss of exon 2
lower sequence: AC149818.2_FGT006 (Zea mays), 5'ss of exon 2
GATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGAgtaaattctcctttgtttttatctttgttacatgttttgaagctttttgtgaattgttttttgtgaaaaaagttgggttgctattgtgggtatgtggtaa---
||||||||| |||||||||||||||||| | || ||||| ||||| ||||| | ||| | || | ||| || || || |||| | || | | | | |||||| || | | || || | | || | | |||| | | ||
GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAAgtacggatta-ttaacgcaaaaggacgatttaggttttgtttctatg-gccgatgattctgtagctcctggtttatgat-ctatatagaccgaagtgcaagtc
upper sequence: GLYMA16G03940.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G053764_T03 (Zea mays), 5'ss of exon 2
GATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGAgtaaattctcctttgtttttatctttgttacatgttttgaagctttttgtgaattgttttttgtgaaaaaagttgggt-tgctattgtgggtatgtggtaa-
||||||||| |||||||||||||||||| | || ||||| ||||| || || | || | ||| | || || || ||||| | | | | ||| ||| | | |||| | | | || | | ||| | || | || | | | | | || || |
GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccctcgcgctga-atcccggttgc-tcttttctctccctgcctcccgtgctgatggtgcacgctcctgattctgatctagatgttgtggggggaa
upper sequence: GLYMA16G03940.2 (Glycine max), 5'ss of exon 2
lower sequence: PP1S37_166V6.1 (Physcomitrella patens), 5'ss of exon 2
GATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGAgtaaattctcctttgttttta--tctttgttacatgttttgaagctttttgtgaattgttttttgtgaaaaaagttgggttgctattgtgggtatgtggtaa
||||||||||||||||||||| |||||| | |||||||||||| || || |||||| | || |||||||| |||||||| || | | | || | || | | |||| | | | | | || | ||| || ||| | ||| | | | | | |
GATGATGAGTGACTACAAGGTCGAGATGGTGAATGATGGAATGAGCGAATTCTATGTGGAGTTTCATGGACCGCGTGAGAgtacgttttttcatttcttaaattcactcctttctgttgcggaccgtatgcgtaactatttcgagttgtgtaaggccgtttg-tgaagctgatgctcgatg-
upper sequence: GLYMA16G03940.2 (Glycine max), 5'ss of exon 2
lower sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 2
GATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGAgtaaattctcc----tttgtttttatctttgttacatgttttgaagctttttgtgaattgttttttgtgaaaaaagttgggttgctattgtgggtatgtggtaa
|||||||||||||||||||||||||||| | || ||||| ||| | |||||| ||||| | ||||||||||| || ||||| | |||| | | || |||| | | | | |||| ||| | | | | | ||| | | |||
GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaagtcctccacactgccctcttctcttcctcttgtctccctgtggttttcgtgcctctgtgtctctcggcttgtttgaaagagagatttcttcttgtt----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|7233955|gb|AW569297.1|AW569297EST: TAATGATGGAATGCAAGAGTTATATGTGCACTTCCATGGACCCAATGAGA GTCCTTATCATGGAGGTGTATGGAAAGTAAGAGTTGAGCTGCCAGATGCTT
genomic: TAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGAgtaaattctc ... ttgcttgcagGTCCTTATCATGGAGGTGTATGGAAAGTAAGAGTTGAGCTGCCAGATGCTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGAgtaaattctcctttgtttttatctttgttacatgttttgaagctttttgtgaattgttttttgtgaaaaaagttgggttgctattgtgggtatgtggtaa
- - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtggg