Sequence
atgc intronic sequence ATGC exonic sequencegtatctatttctatttctcactcctcttaagtgcacgcacatgtgaaaagactattgactcatgaataaagttctggtgcttggatctccattttatggttgacattaaccgtgcctactgttgaccgtgcagCTTGGAGCTGTTGCGGCACTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCTG
Basic information
species | Glycine max |
transcript | GLYMA20G38980.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G38980.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g67340.3 (Oryza sativa), 3'ss of exon 7
gtatctatttctatttctcactcctcttaagtgcacgcacatgtgaaaagactattgactcatgaataaagttctggtgcttggatctccattttatggttgacattaaccgtgcctactgttgaccgtgcagCTTGGAGCTGTTGCGGCACTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGA--AGTCTCCTG
|||| || || ||||| || || | | | || ||| |||||| || || | ||| | | | | || || || | | | | || | ||||||||| ||| ||||| ||| ||||||| || || |||||||||||| | ||||| ||||||||||| || || || | ||||| || | ||| |
--------------gtctcgatctctatacatgcacaca-atatttatacaca--tgagtcatga-tagtcatcctttccttctcttttc-ccccacatttctcacta-ctgcactttct-----cgatgcagCTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCAAACATGAGCATTGTGGTGAAGGCTTTATCTCCACTGCTCACAAGTAAGC--
upper sequence: GLYMA20G38980.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G029530_T01 (Zea mays), 3'ss of exon 7
gtatctatttctatttctcactcctcttaagtgcacgcacat--gtgaaaagactattgactcatgaataaagttctggtgcttggatctccattttatggttgacattaaccgtgcctactgttgaccgt-gcagCTTGGAGCTGTTGCGGCACTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCTG
||| | | | || | ||| |||| || | | || | || || || | | || || | | | ||| | ||| ||| ||| | ||| || || | || |||||||| ||||| ||||||||||| ||||| |||||| |||| ||||| || | |||||||| || ||||| |||||| ||| ||||| | |
--gtctggcttcaatccttccataccttgtgtgcgtgcgcttccatgggttggttactgcaatctgctatacgatcaggaaggcagtaagcaactttgttgtttacactaaatggtcct-cttctgtctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCCAGCATGAGCATCGTAGTTAAGGCACTCTCACCCCTTCTTCAACATAAAC
upper sequence: GLYMA20G38980.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G071877_T01 (Zea mays), 3'ss of exon 7
gtatctatttctatttctcactcctcttaagtgcacgcacatgtgaaaagactattgactcatgaataaagttctggtgcttggatctccattttatggttgacattaaccgtgcctactgttgaccgtgcagCTTGGAGCTGTTGCGGCACTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCTG
|| | | | || || || |||| |||||| | || || || ||| |||| || |||||| | || || | | ||| | || ||||||||| || || || |||||||| ||||| || ||||| ||||| ||||| || |||||||||||||| || || || || || || |
--------gtcaacattttaccccctc---gtacacgtctctgtgaatgatgtttttac--attaat-------------ttggccatc--ttttattgatgtaatcc-ctttcccttggactctccctgcagCTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCCAACATGAGCATTGTTGTGAAGGCGCTTTCGCCTCTCCTTCAACAAAGAC
upper sequence: GLYMA20G38980.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G59350.3 (Arabidopsis thaliana), 3'ss of exon 5
gtatctatttctatttctcactcctcttaagtgcacgcacatgtgaaaagactattgactcatgaataaagttctggtgcttggatctccattttatggttgacattaaccgtgcctactgttgaccgtgcagCTTGGAGCTGTTGCGGCACTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCTG
|||| ||| || | | | | | | | | || |||| ||| | | | || | | | | ||| |||| | | | | ||||| | || || || ||| |||| ||||| |||||| | |||||||||||||| ||||||||||| || ||||| || |||||| | ||| ||| |
gtataagcttcatctttttgacagtttaatctata-acccctgcgaaaccactttcaaaacgctaacca------------taaaatactgtttc------------------gccttgttcttgcgcttcagCTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCAAACATGAGCATTGTGGTAAAAGCTCTTCAACCATTGTTGAGGTCATCAA
upper sequence: GLYMA20G38980.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G43230.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatctatttctatttctcactcctcttaagtgcacgcacatgtgaaaagactattgactcatgaataaagttctggtgcttggatctccattttatggttgacattaaccgtgcctactgttgaccg-tgcagCTTGGAGCTGTTGCGGCACTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCTG
| | ||| | | ||| | |||| | | | ||| ||| | ||| || | | | || ||| | || || | ||||||| ||| ||||| || |||| ||||| || ||||| |||||||||||||| ||||||||||| || ||||| || ||||| || ||| ||| |
------------------------------------gta-atgaacagaaacttcctagtcatttaaataactctagtg-----gaccccacttacaagctaaaat-----gtgtgttttgatggtaaatacagCTTGCAGCGGTTGCAGCGTTGTGTGTGCAATACGAAGCAGAGTTTAGGCCAAACATGAGCATTGTAGTAAAAGCTCTTCAACCGCTCTTGAGGTCAGCAA
upper sequence: GLYMA20G38980.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 7
gtatctatttctatttctcactcctcttaagtgcacgcacatgtgaaaagactattgactcatgaataaagttctggtgcttggatctccattttatggttgacattaaccgtgcctactgttgaccgtgcagCTTGGAGCTGTTGCGGCACTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCTG
|| ||| | || | |||| ||| ||| ||| |||| ||||| | ||| || || | ||| | || | || | ||||||| | |||||| || ||| | || || ||||| ||||||||||| |||||||||||||||| ||||| || || |||||||| ||| | ||| || |||
gtctctttgcctctctctctctc-tctctctctcacccacacacac-----------actcacagaaaaataactagtagctaactct----------------gtgaattg--------gtgggtgatgcagCTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCAAATATGAGCATCGTTGTGAAGGCTCTCCAACCGCTTTTAAAGGCTGCTGMapped 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|19053775|gb|BM732442.1|BM732442EST: GCGTTGACCCAAAACTGAAGGGAGAATANNNNNNNAAAGGAGTTGCTAAG CTTGGAGCTGTTGCGGCACTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
genomic: GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCCAAAGGAGTTGCTAAGgtatctattt ... gaccgtgcagCTTGGAGCTGTTGCGGCACTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
EST:
gi|8669663|gb|BE190770.1|BE190770EST: GCGTTGACCCAAAACTGAAGGGAGAATANNNNNNNAAAGGAGTTGCTAAG CTTGGAGCTGTTGCGGCACTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
genomic: GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCCAAAGGAGTTGCTAAGgtatctattt ... gaccgtgcagCTTGGAGCTGTTGCGGCACTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttggatctccattttatggttgacattaaccgtgcctactgttgaccgtgcagCTTGGAGCTGTTGCGGCACTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCTG
attttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctatttctatttctcactcctcttaagtgcacgcacatgtgaaaagactattgactcatgaataaagttctggtgcttggatctccattttatggttgacattaaccgtgcctactgttgaccgtgcagCTTGGAGCTGTTGCGGCACTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG