Sequence
atgc intronic sequence ATGC exonic sequencegtaacataggttctaagctatcccttttcacttttccatgtatgccccgcttgtccatttatatatgttaaattgaagcgtctcttcgaatcctttgcagATAGATGCTGCGATAAATTCTGGGAATTCTGGTGGACCTGCTTTCAATGATAAGGGAAAATGCGTTGGGATTGCATTCCAGTCTCTTAAACATGAAGATG
Basic information
species | Glycine max |
transcript | GLYMA01G16820.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G16820.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g12780.1 (Oryza sativa), 3'ss of exon 2
----------------------------------------gtaacataggttctaagc-tatcccttttcacttttccatgtatgccccgcttgtccatttatatatgt-taaattgaagcgtctcttcgaatcctttg-cagATAGATGCTGCGATAAATTCTGGGAATTCTGGTGGACCTGCTTTCAATGATAAGGGAAAATGCGTTGGGATTGCATTCCAGTCTCTTAAACATGAAGATG
| | || || | || || || || | | | || || | | | | | | ||| | || | || | ||||||||||| || |||||||| || || ||||| || |||||||| ||||||||||| || || || || || || || || ||||||||||| |||||||
gtttttctcttaagatctttgcatgcttttgattgtctatattttgcatattgtagacatagtttttacttctctttggaattatttctaataatctcttaacctgggagcatacttaagt-tttcactgtttcatggaacagATAGATGCAGCTATAAATTCAGGAAACTCTGGGGGCCCTGCTTTTAATGATAAGGGCAAGTGTGTGGGCATAGCTTTTCAATCTCTTAAACACGAAGATG
upper sequence: GLYMA01G16820.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G165969_T01 (Zea mays), 3'ss of exon 3
-------------gtaacataggttctaagctatcccttttcacttttccatgtatgccccgcttgtccatttatatatgttaaattgaagcgtctcttcg--aatcctttgcagATAGATGCTGCGATAAATTCTGGGAATTCTGGTGGACCTGCTTTCAATGATAAGGGAAAATGCGTTGGGATTGCATTCCAGTCTCTTAAACATGAAGATG
||| ||| | | || | ||| | ||| || | ||| | | | ||||| || || |||| || | || | ||||||||||| || |||||||| || ||||| || || |||||||||||||||||||||||||| ||||| || || ||||| |||||||||||||||||||
gtattaacgtattgtattatattctgcatacttttacttatagatttgccttttatacgttgaactatgccacacttatgtaaacttctgttgtctgtttattactcataaacagATAGATGCAGCTATAAATTCAGGAAATTCAGGGGGGCCTGCTTTCAATGATAAGGGAAAATGTGTTGGTATAGCTTTCCAATCTCTTAAACATGAAGATG
upper sequence: GLYMA01G16820.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G877597_T02 (Zea mays), 3'ss of exon 2
------------------gtaacataggttctaagctatcccttttcac-------ttttccatgta---tgccccgcttgtccatttat-atatgttaa---attgaagcgtct----cttcgaatcctttgcagATAGATGCTGCGATAAATTCTGGGAATTCTGGTGGACCTGCTTTCAATGATAAGGGAAAATGCGTTGGGATTGCATTCCAGTCTCTTAAACATGAAGATG
|| ||| ||| || ||| ||| | | || || || | ||| | | || | | | | || | |||| | | | | || |||||||||| || || ||||| || ||||| ||||| || ||||| ||||||| ||||||||| || || || || || ||||||||||||||||||||||
gtacatttttttctgaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaaatattttgagaaatcatgacttatcggctcaccgacgtgtctaataccttgtcttgttaatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
upper sequence: GLYMA01G16820.1 (Glycine max), 3'ss of exon 2
lower sequence: AC212112.4_FGT002 (Zea mays), 3'ss of exon 2
--------------------gtaacataggttctaagctatcccttttcac-------ttttccatgt---atgccccgcttgtccatttat-atatgttaa---attgaagcgtct--------cttcgaatcctttgcagATAGATGCTGCGATAAATTCTGGGAATTCTGGTGGACCTGCTTTCAATGATAAGGGAAAATGCGTTGGGATTGCATTCCAGTCTCTTAAACATGAAGATG
|| ||| ||| || ||| ||| | | || || || | | ||| | || | | | | || | |||| | | | | || |||||||||| || || ||||| || ||||| ||||| || ||||| ||||||| ||||||||| || || || || || ||||||||||||||||||||||
gtacattttttttcctgaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaactattttgagaaaccatgacttatcggctcaccgacgtgtctaatacgggccttgtcttgttgatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
upper sequence: GLYMA01G16820.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G015959_T01 (Zea mays), 3'ss of exon 2
-------------------gtaacataggttctaagctatcccttttcac-------ttttccatgt---atgccccgcttgtccatttat-atatgttaa---attgaagcgtct--------cttcgaatcctttgcagATAGATGCTGCGATAAATTCTGGGAATTCTGGTGGACCTGCTTTCAATGATAAGGGAAAATGCGTTGGGATTGCATTCCAGTCTCTTAAACATGAAGATG
|| ||| ||| || ||| ||| | | || || || | ||| | | || | | | | || | |||| | | | | || |||||||||| || || ||||| || ||||| ||||| || |||| ||||||| ||||||||| || || || || || ||||||||||||||||||||||
gtacattttttctctaaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaaatattttgagaaatcatgacttatcggctcaccgacgtgtctaatacgggccttgtcttgttaatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAACTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
upper sequence: GLYMA01G16820.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G144501_T02 (Zea mays), 3'ss of exon 2
-------------------gtaacataggttctaagctatcccttttcacttttccatgt---atgccccgcttgtccatttatatatgttaa-----------attgaagcgtct--------cttcgaatcctttgcagATAGATGCTGCGATAAATTCTGGGAATTCTGGTGGACCTGCTTTCAATGATAAGGGAAAATGCGTTGGGATTGCATTCCAGTCTCTTAAACATGAAGATG
|| ||| ||| || | | | | | | |||| | | | || ||| | | || ||| | | |||| | | | | || |||||||||| || || ||||| || ||||| ||||| || ||||| ||||||| || ||||| || || || ||||| || |||||||||||||||||||
gtacctttcccccctgaaattataataacttcaaataaacctttatataaagatggatgttgcaagtgaagtaaatctattgagaaataataacttatctgcttaccggcatgtctaatacgggccttgtcttgttgatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGTCCAGCTTTTAATGATAGAGGCAAATGTGTCGGTATAGCATTTCAATCTCTTAAACATGAAGATG
upper sequence: GLYMA01G16820.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0066g01660.t01 (Vitis vinifera), 3'ss of exon 2
gtaacataggttctaagctatcccttttcacttttccatgtatgccccgcttgtccatttatatatgttaaattgaagcgtctctt-cgaat--cctttgcagATAGATGCTGCGATAAATTCTGGGAATTCTGGTGGACCTGCTTTCAATGATAAGGGAAAATGCGTTGGGATTGCATTCCAGTCTCTTAAACATGAAGATG
|| |||| ||| | || | ||| | | || | | | | | ||| | ||||| || | || | | |||||||||||||||||| ||||| ||||| ||||||||||||||||| | |||||||| || ||||| || || || ||||| ||||| ||||||||||||||||
gtttcatatgttt---gttacatataaacacactcctttgcctatctaacaggaaaaaaattatgtcttaaacattcttgttgttcatgagttgcttttgcagATAGATGCTGCAATAAACTCTGGAAATTCTGGTGGACCTGCAATTAATGATAAAGGCAAATGTGTGGGTATCGCATTTCAGTCCCTTAAACATGAAGATG
upper sequence: GLYMA01G16820.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S176_87V6.1 (Physcomitrella patens), 3'ss of exon 3
--gtaacataggttctaagctatcccttttcacttttccatgtatgccccgcttgtccatttatatatgttaaattgaagcgtctcttcgaatcctttgcagATAGATGCTGCGATAAATTCTGGGAATTCTGGTGGACCTGCTTTCAATGATAAGGGAAAATGCGTTGGGATTGCATTCCAGTCTCTTAAACATGAAGATG
| | | | || || ||| || | || ||||| | | || | ||| | | | | | ||||||| |||||||| |||||| ||||||| ||||| || ||||||||||| || | || ||||||| || || || || ||||| || || || || ||||
tctcagcgcacat-ctgttgcatgggtttctttggttttggggttgtgggacttgttt-tggggagttgctggatttacttgctttcttggtgggaatgcagATTGATGCTGCTATAAATGCTGGGAACTCTGGAGGCCCTGCTTTCAACGACAGAGGTGAATGCGTGGGAATCGCTTTTCAGTCGCTGAAGCACGAGGATGMapped 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|15203292|gb|BI426060.1|BI426060EST: TGGAGATACTCTCTTATGTTCATGGTTCAACGGAACTTCTGGGACTGCAG ATAGATGCTGCGATAAATTCTGGGAATTCTGGTGGACCTGCTTTCAATGAT
genomic: TGGAGATACTCTCTTATGTTCATGGTTCAACGGAACTTCTGGGACTGCAGgtaacatagg ... tcctttgcagATAGATGCTGCGATAAATTCTGGGAATTCTGGTGGACCTGCTTTCAATGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccgcttgtccatttatatatgttaaattgaagcgtctcttcgaatcctttgcagATAGATGCTGCGATAAATTCTGGGAATTCTGGTGGACCTGCTTTCAATGATAAGGGAAAATGCGTTGGGATTGCATTCCAGTCTCTTAAACATGAAGATG
tcctttgc CT-rich tract
atttatatatgttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacataggttctaagctatcccttttcacttttccatgtatgccccgcttgtccatttatatatgttaaattgaagcgtctcttcgaatcctttgcagATAGATGCTGCGATAAATTCTGGGAATTCTGGTGGACCTGCTTTCAATGATAAGGGAAAATGCGTTGGGATTGCATTCCAGTCTCTTAAACATGAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG