Sequence
atgc intronic sequence ATGC exonic sequencegtacaatgtaatctttctattcctttctaatcaggactttttcactagcctgttttggttccttaatacatctatagGTAGGGCCTCTTCGCTGTTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACAGACGTGGGAGAATTTATTGTCCCAATACCACATGTCAAGC
Basic information
species | Glycine max |
transcript | GLYMA10G29060.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G29060.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g18970.1 (Oryza sativa), 3'ss of exon 3
-------------------------gtacaatgtaatctttctattcctttctaatcaggactttttcactag----cctgttttggttccttaatacatctatagGTAGGGCCTCTTCGCTGTTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACAGACGTGGGAGAATTTATTGTCCCAATACCACATGTCAAGC
| || | | | |||| | || | | ||| ||| || || | || ||| | | ||||| || ||||| | || ||||| ||||||||||||||||| ||||| ||||| || || ||||| || || || ||||| ||||| |||||||||||||
gtaagctgctagtaaatattcttggaaagaacttcaaggatacattcaatgctgtcaaagcatttctcattatgggttttgatgtgaaatcttgctgttgttttagGTGGGACCTCTCAGATGCTGGCCAGGTGGATTGTGCCTTTCAAGATCGATTGGGGATACTGACGTTGGGGAGTTCATTGTGCCAATTCCACATGTCAAGC
upper sequence: GLYMA10G29060.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G006429_T01 (Zea mays), 3'ss of exon 3
--------------------------------------------gtacaatgtaatctttctattcctttctaatcaggactttttcactagcctgttttggttccttaatacatctatagGTAGGGCCTCTTCGCTGTTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACAGACGTGGGAGAATTTATTGTCCCAATACCACATGTCAAGC
|||||| | | || |||| | || || | || | || | | ||| | || | | | ||||| || ||||| || || ||||| ||||||||||||||||| || |||||||| || || || || || || || ||||| || || |||||||||||||
gtagtgctcactgctcagtcattttgatgaagaaggattctaggatacaatatgagct--ctatgctttggaaac----atttctgcatgggattttttaattaatttctcccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGC
upper sequence: GLYMA10G29060.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G113016_T01 (Zea mays), 3'ss of exon 3
------------------gtacaat--gtaatctttctattcctttctaatc--aggactttttcactagcctgttttggttccttaatacatcta--tagGTAGGGCCTCTTCGCTGTTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACAGACGTGGGAGAATTTATTGTCCCAATACCACATGTCAAGC
|| | |||| | ||| | |||| | || | | || | | || || | | ||||| || ||||| || || ||||||||||| ||||||||||| ||||| ||||| |||| || || || || | ||||| || || |||||||||||||
gtaaaccagttcaattcgagtcagttagtaacttccttatcctcaatcaatcgtacgagcatcttgctgatgcactgttgtatgtttttttgggaaattagGTTGGTCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTTTCAAGATCCATTGGGGACATGGATGTTGGGGAGTACATTGTGCCCATTCCACATGTCAAGC
upper sequence: GLYMA10G29060.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G09160.2 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------------------gtacaatgtaatctttctattcctttctaatca--ggacttttt----cactagcctgttttggttcc-ttaatacatctatagGTAGGGCCTCTTCGCTGTTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACAGACGTGGGAGAATTTATTGTCCCAATACCACATGTCAAGC
| || || || | | || ||| ||| | || || |||| || ||| || |||||| || || || || || ||||||||||| || || ||||| || || |||||||| || || |||||||||||||||||||| |||||||| || ||||
gtatgatcatttccagtgaatttaagttactgtttcattgtgttttggctgtggtgggtttgtaatgtgtaagaagtccttggattttcaatgatattaatgtgctttgattatgccaatgca---atagGTCGGCCCACTACGATGCTGGCCTGGTGGTTTATGTCTTTCGAGGTCCATTGGTGATACGGATGTGGGAGAATTTATTGTCCCTATACCACACGTTAAGC
upper sequence: GLYMA10G29060.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 4
gtacaatgtaatc--tttctattcctttctaatc----aggactttt------tcactagcctgttttggttcctta--------atacat-----ctatagGTAGGGCCTCTTCGCTGTTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACAGACGTGGGAGAATTTATTGTCCCAATACCACATGTCAAGC
||| || || | | | || | || || | || | |||| | | | | ||| ||| || | | || || | ||||| || || || ||||| |||||||||||||| || || || || ||||||||||||||||| ||||||||||| |||||||||||||||||||| ||||
gtataacatatttgatgcccatacaactcaaagctgaaagaaattttaattgattattcccttgtcttgaatcttcatgggtcaaatgtatatggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATTGGTGACACAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGCMapped 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|6134100|gb|AW132493.1|AW132493EST: CTGCCAGTGGTGGTGAAGTAGGAAGACTCAATGTATTTGGAGGCAATGAG GTAGGGCCTCTTCGCTGTTGGCCTGGTGGATTGTGCCTTTCTAGATCAATT
genomic: CTGCCAGTGGTGGTGAAGTAGGAAGACTCAATGTATTTGGAGGCAATGAGgtacaatgta ... acatctatagGTAGGGCCTCTTCGCTGTTGGCCTGGTGGATTGTGCCTTTCTAGATCAATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttctaatcaggactttttcactagcctgttttggttccttaatacatctatagGTAGGGCCTCTTCGCTGTTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACAGACGTGGGAGAATTTATTGTCCCAATACCACATGTCAAGC
ttaatacatctata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaatgtaatctttctattcctttctaatcaggactttttcactagcctgttttggttccttaatacatctatagGTAGGGCCTCTTCGCTGTTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACAGACGTGGGAGAATTTATTGTCCCAATACCACATGTCAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA