Sequence
atgc intronic sequence ATGC exonic sequenceAAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCGgtaattcctttaactttataatgttataggcaagatggatatgctgataaataattttttaagactttatatatctcaactctcaagaaacattgatgta...
Basic information
species | Glycine max |
transcript | GLYMA12G06980.2 |
intron # | 8 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G06980.2 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os03g16980.3 (Oryza sativa), 5'ss of exon 8
AAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCGgtaat--tcctttaact--ttataatgttataggcaagatggatat-gctgataaataattttttaagactttatatatctcaactctcaagaaacattgatgta
| || || ||||| || || || ||||| |||||||| | ||||| |||||||||||||||||||| ||||||||||| ||||| || | ||||||| || | |||| || || || | || | || | | || | | || | || ||| || || | | ||
AGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcgctgaacttctttcaacattctct-caggttgtgtccagttggtcctggagcttat----tttcatacat---aattttacag-------------
upper sequence: GLYMA12G06980.2 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 9
AAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCGgtaat--tcctttaacttt-----ataatgttataggcaagatggatatgctgataaataattttttaagactttatatatctcaactctcaagaaacattgatgta
| || || ||||| || || || ||||| |||||||| | ||||| |||||||||||||||||||| ||||||||||| ||||| || | ||||||| || | ||||| | | | | ||| | | || | | | | |||| | |
AGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTTgttagtaacttcattgctcaggccgtacggtaatgctcgctgaacttctttcaacattctctcaggttgtgtccagttggtcctggagcttattttcata------------------------------------
upper sequence: GLYMA12G06980.2 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G177373_T02 (Zea mays), 5'ss of exon 9
AAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCGgtaattcct--ttaactttataatgttat------aggcaagatggatatgctgataaataattttttaagactttatatatctcaactctcaagaaacattgatgta
|||| || ||||| || || |||||||| ||||| || | ||||| ||||||||||| |||||||| || |||||||| ||||| || | ||||||| | | || | | ||| | || | || | ||||| || |||| |||| | | | | ||
AAATCCGGATTGCCAGGATTTTTAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgctttgttgaatgtattttattttctcttgagctactgcagatatattggcggctaatcttttcacaatctttag----------------------------
upper sequence: GLYMA12G06980.2 (Glycine max), 5'ss of exon 8
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 8
AAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCGgtaattcctttaactttataatgttataggcaagatggatatgctgataaataattttttaagactttatatatctcaactctcaagaaacattgatgta
|||| |||||||| |||||||| ||||| ||||| ||||||||||| || |||||||| |||||||| || |||||||| || |||||| | |||| | | || || ||| | ||| | || | | || |||| || | | || | ||| | ||| ||| ||
AAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCGgtgagcctctttgct---caatccaacgaacaaattttattttccgagctataaattactcatctcttgt-tattgttcttgtcatgaatacttag----
upper sequence: GLYMA12G06980.2 (Glycine max), 5'ss of exon 8
lower sequence: AT2G28760.3 (Arabidopsis thaliana), 5'ss of exon 7
AAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCGgtaa-------ttcctttaactttataatgttataggcaagatggatatgct-----gataaataatt------ttttaagactttatatatctcaactctcaagaaacattgatgta----------------------
| |||||||| ||||| || || ||||||||||| || || ||||| ||||||||||| || ||||| || |||||||| ||||| || | ||| | ||| | || || | | |||| | | | | | ||||| |||| || | || || ||| ||| ||| | |
AGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAGgtgaaactaatctccatcaagttcttgaatttatcttttttttttttttttttcttgaaaaaatagccgagtaattttgagtcgaatcctagactaattctaaagcctttttgtttgataaaattgttttgggtttgcag
upper sequence: GLYMA12G06980.2 (Glycine max), 5'ss of exon 8
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 5'ss of exon 8
AAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCGgtaattcctttaactttataatgttataggcaagatggatatgctgataaataattttttaagactttatatatctcaactctcaagaaacattgatgta-
|||| |||||||| |||||||| ||||||||||| || || ||||| || ||||||||||||||||| || |||||||| ||||||||| | |||||| | ||| || | | | || || || | || | ||| || || | || || | || ||| | | ||||
AAATCCGCATTGCTAGAATCTTCAACACATATGGTCCTCGAATGAACATCGATGATGGGCGTGTTGTGAGCAACTTCATTGCTCAAGCACTCCGgtaaagtcattagctctctcaacttc--------attgaaac-----caagt--tttgtttcatctctgcttagctgtgtttccattaaatgt-gttgtag
upper sequence: GLYMA12G06980.2 (Glycine max), 5'ss of exon 8
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 5'ss of exon 9
AAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCGgtaattcctttaactttataatgttataggcaagatggatatgctgataaataattttttaagactttatatatctcaactctcaaga-aacattgatgta---
||||||||||||| ||||| || ||||||||||| || |||||||||||||||||||| ||||||||||| || ||||| ||||||||| ||||||| ||||| | | | | | | || || ||| | || ||| | | | | | || | ||||| |||| | |
AAATACGCATTGCTAGAATTTTCAACACATATGGGCCCCGCATGAATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCGgtatgtccttatgtagtccttagctgttgatcatatttgtaagct----actattttcatttaatcatgctttgtttaatttccaagatgacatccactgaact
upper sequence: GLYMA12G06980.2 (Glycine max), 5'ss of exon 8
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 9
AAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCGgtaattcctttaactttataatgttataggcaagatggatatgctgataaataattttttaagactttatatatctcaactctcaagaaacattgatgta---
|||| || | || |||| |||||||| ||||| || ||||||||||| || |||||||| || ||||| || || || ||||||||| | |||| | | | | | | | || | |||| ||| | | | ||| | | || | | || || | | |||
AAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGgta-----ctggtcctcaaggtctca-----aaattcaatatttccttaacttaat-----gaactcaacacatttga-----catgatgtacgggtgtgtagMapped 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|209703510|gb|BW656548.1|BW656548EST: AATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCG TGGTGAACCCTTAACTGTCCAAGTTCCAGGAACTCAAACTCGCAGTTTTTG
genomic: AATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCGgtaattcctt ... tgtgttacagTGGTGAACCCTTAACTGTCCAAGTTCCAGGAACTCAAACTCGCAGTTTTTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCGgtaattcctttaactttataatgttataggcaagatggatatgctgataaataattttttaagactttatatatctcaactctcaagaaacattgatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA