Sequence
atgc intronic sequence ATGC exonic sequence...cactgtgcaattatgtaataatccctattcatgtatcttagttattcatttgctttcaatatgctcaaaaccttgacattgatataaaatttgatttcagGCCATACCTGATTATTTGGAGAACTGTAGATTTCTTCCAGTGCTTAACAATGAAATACCAGATAAGAGAAATTCTACTTACAAGGAAAGATTTAGTAGCT
Basic information
species | Glycine max |
transcript | GLYMA01G41570.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G41570.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g01150.1 (Oryza sativa), 3'ss of exon 9
cactgtgcaattatgtaataatccctattcatgtatcttagttattcatttgctttcaatatgctcaaaaccttgacattgatataaaatttg-----atttcagGCCATACCTGATTATTTGGAGAACTGTAGATTTCTTCCAGTGCTTAACAATGAAATACCAGATAAGAGAAATTCTACTTACAAGGAAAGATTTAGTAGCT
| | ||| | ||||| || || | || | | |||| || ||| | || | ||| || |||| || ||||||| || | |||||||| || ||||||||||||||| |||||||||||| |||||| | | |||||| | || ||||||||||| ||||| ||||
-tttcttcaag-gcatgataattactggaaatagaatttgat-gtgtatttatgtt-aatgt-ttcgattaactgaagtttgcataaccttcctatgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCT
upper sequence: GLYMA01G41570.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G374779_T03 (Zea mays), 3'ss of exon 9
cactgtgcaattatgtaataatccctattcatgtatcttagttattcatttgctttcaatatgctcaaaaccttgacattg---atataaaatttgatttcagGCCATACCTGATTATTTGGAGAACTGTAGATTTCTTCCAGTGCTTAACAATGAAATACCAGATAAGAGAAATTCTACTTACAAGGAAAGATTTAGTAGCT
|| | | | ||| | | | |||||| ||||| | | | ||| | | | ||| | ||||| | | ||||| || | |||||| || ||| ||||| ||||||||| |||||||||||||| |||||||| |||||| | || |||||||||||||| |||||||
--ttgattattagtacaattaaatttgt-catgtaatatagtttcatagtatatgagaatgtttctggtgcacgaagtttgtctaactaaaagtatgtatcagGATATGGCAGATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAATGAAATTCCAGATAAAAGAAATGCCACCTACAAGGAAAGATTCAGTAGCT
upper sequence: GLYMA01G41570.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G374779_T04 (Zea mays), 3'ss of exon 5
cactgtgcaattatgtaataatccctattcatgtatcttagt-tattcatttgctttcaatatgctcaaaaccttgacattgatataaaatttgatttcagGCCATACCTGATTATTTGGAGAACTGTAGATTTCTTCCAGTGCTTAACAATGAAATACCAGATAAGAGAAATTCTACTTACAAGGAAAGATTTAGTAGCT----------
|| |||||| | | || | || || |||| ||| || || | || | || | | | ||||| | | ||||| || | |||||| || ||| ||||| ||||||||| |||||||||||||| |||||||| |||||| | || |||||||||||||| |||||||
----gtacaattaaatt-tgtcatgtaatatagtttcatagtatatgagaatgtttctggt--gcacgaagttt----gtctaactaaaagtatgtatcaggatatggcagATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAATGAAATTCCAGATAAAAGAAATGCCACCTACAAGGAAAGATTCAGTAGCTTAGAGAATTTMapped 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|5761044|gb|AI966407.1|AI966407EST: CTTAAATTACCGAAT GCCATACCTGTTTATTTGGAGAACTGTAGATTTCTTCCAGTGCTTAACAAT
genomic: CTTAAATTACCGAATgtgagttgca ... ttgatttcagGCCATACCTGATTATTTGGAGAACTGTAGATTTCTTCCAGTGCTTAACAAT
EST:
gi|21285430|gb|BQ473301.1|BQ473301EST: GAACACTTGGCTCCTAGTGGATATCTTAAATTACCGAAT GCCATACCTGATTATTTGG
genomic: GAACACTTGGCTCCTAGTGGATATCTTAAATTACCGAATgtgagttgca ... ttgatttcagGCCATACCTGATTATTTGG
EST:
gi|9901990|gb|BE610958.1|BE610958EST: GAACACTTGGCTCCTAGTGGATATCTTAAATTACCGAAT GCCATACCTGATTATTTGGAGAACTGTAGATTTCTTCCAGTGCTTAACAAT
genomic: GAACACTTGGCTCCTAGTGGATATCTTAAATTACCGAATgtgagttgca ... ttgatttcagGCCATACCTGATTATTTGGAGAACTGTAGATTTCTTCCAGTGCTTAACAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatttgctttcaatatgctcaaaaccttgacattgatataaaatttgatttcagGCCATACCTGATTATTTGGAGAACTGTAGATTTCTTCCAGTGCTTAACAATGAAATACCAGATAAGAGAAATTCTACTTACAAGGAAAGATTTAGTAGCT
acattgatataaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cactgtgcaattatgtaataatccctattcatgtatcttagttattcatttgctttcaatatgctcaaaaccttgacattgatataaaatttgatttcagGCCATACCTGATTATTTGGAGAACTGTAGATTTCTTCCAGTGCTTAACAATGAAATACCAGATAAGAGAAATTCTACTTACAAGGAAAGATTTAGTAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
-actgtgc
- - - - - - - - - - - - - - -catgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaacc