Sequence
atgc intronic sequence ATGC exonic sequence...atttatttattattagctggtgatcggtgctttttcattcgttatgattctatttctgtttcctattctgttgttgattctgatgttaaatgttttgcagCTCGTACGCAGCAACAGTCGGCGGTTTATGCCGTCCCAGGCTGATGAAGAGGCACATCAATTGTCGTATCTGCAAAAGCACTTGGCTAACATTGTGTCTC
Basic information
species | Glycine max |
transcript | GLYMA03G29860.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G29860.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g41110.1 (Oryza sativa), 3'ss of exon 1
---atttatttattattagc-tggtgatcggt-gctttttcattcgttatgattctatttctgtttcctattctgttgttgatt-ctgatgttaaatgttttgcagCTCGTACGCAGCAACAGTCGGCGGTTTATGCCGTCCCAGGCTGATGAAGAGGCACATCAATTGTCGTATCTGCAAAAGCACTTGGCTAACATTGTGTCTC
|| | | ||| | || | | || | ||| |||| || || ||| || | | || ||| | ||||||| | ||||||| |||||||| |||||||| ||||||||||| || || || |||||||| || |||||||| || |||||||||||||| ||| |||||| || ||
cttgctttactcctgctagtgcagagaccaacagtttctatatttgttac--ttgtaagggcctttttaatattaatcttcattgtttatgttaa----tatgcagCTTGTACGCAGTAACAGTCGCCGGTTTATGCCTTCACAAGCAGATGAAGAAGCTCATCAATTATCTTATCTGCAAAAGCATATGGTCAACATTCTGAGTC
upper sequence: GLYMA03G29860.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G417658_T02 (Zea mays), 3'ss of exon 1
atttatttattattagctggtgatcggtgctttttcattcgttatgattctatttc-tgtttcctattctgttgttgattctgatgttaaatgttttgcagCTCGTACGCAGCAACAGTCGGCGGTTTATGCCGTCCCAGGCTGATGAAGAGGCACATCAATTGTCGTATCTGCAAAAGCACTTGGCTAACATTGTGTCTC
| | | | || | | | || ||| ||| | | | || | | | | | || | |||| | | | ||||||||||| || ||||| ||||| || || |||||||| || || ||||||||||| ||||| ||||| |||||||||||||| |||| || ||| | |||
-tagctgcgctgccatcttctatttcaagtgattagattgtctataacttaaaatcacatctgatctgcctttaattattccaaactatatggttttgcagCTTGTTCGCAGTAACAGCCGTCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTATCTGCAAAAGCATATGGCGAATATTCTTACTC
upper sequence: GLYMA03G29860.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G180690_T01 (Zea mays), 3'ss of exon 3
atttatttattattagctggtgatcggtgctttttcattcgttatgattct---atttctgtttcctattctgttgttgattctgatgttaaatgttttgcagCTCGTACGCAGCAACAGTCGGCGGTTTATGCCGTCCCAGGCTGATGAAGAGGCACATCAATTGTCGTATCTGCAAAAGCACTTGGCTAACATTGTGTCTC-----------
| || | || ||| | ||| ||| | | | | | | || | || | ||| || ||| || |||||||||| || ||||||||||| || || |||||||| || || ||||||||||| ||||| ||||| | |||||||||||| |||| || ||| | |||
-------------catcttccatttcaaatggttagattggctataattttcaaaatcatctctgacatgcctttaattatttcaat-ttatattttttgcagcttgttcgcagCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTCTCTTGGCAGAT
upper sequence: GLYMA03G29860.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G145376_T01 (Zea mays), 3'ss of exon 1
-attta--tttattattagctggtgatcggtgctttttcattcgttatgattctatttctgtttcctattctgttgttgattctgatgttaaatgttttgcagCTCGTACGCAGCAACAGTCGGCGGTTTATGCCGTCCCAGGCTGATGAAGAGGCACATCAATTGTCGTATCTGCAAAAGCACTTGGCTAACATTGTGTCTC
|||| | | | | || | || ||| | ||| | | | | | | || | || | ||| || ||| || |||||||||| || ||||||||||| || || |||||||| || || ||||||||||| ||||| ||||| | |||||||||||| |||| || ||| | |||
gttttagctgtgctgccatcttccatttcaaatggttagattggctat--tcaaaatcatctctgacatgcctttaattatttcaat-ttatattttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTC
upper sequence: GLYMA03G29860.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G57890.2 (Arabidopsis thaliana), 3'ss of exon 2
atttatttattattagctggtgatcggtgcttttt-cattcgttatgattctatttctgtttcctattctgttgttgat-tctgatgttaaatgttt-tgcagCTCGTACGCAGCAACAGTCGGCGGTTTATGCCGTCCCAGGCTGATGAAGAGGCACATCAATTGTCGTATCTGCAAAAGCACTTGGCTAACATTGTGTCTC
| |||| | || | ||| || || || | | |||| || || ||| | || | ||| ||||||| || ||||||||||| || || |||||||| || ||||| ||||| || || ||||| ||||| ||||||||||| || || || ||||| | ||||
---------------gtattctatcgtttctcatcacatgggtcgaaccaactttattggagctaaaattgttatttatatctccttttcatcatttctgcagCTTGTTCGCAGCAACAGCCGTCGATTTATGCCATCACAGGCAGATGATGAAGCTCATCAGTTGTCATATCTGCAAAAACATTTAGCAAACATCATTTCTC
upper sequence: GLYMA03G29860.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G42230.1 (Arabidopsis thaliana), 3'ss of exon 1
-atttatttattattag-ctggtgatcggtgctttttcattcgttatgattctatttctgtttcctattctgttgttgattctgatgttaaatgttttgcagCTCGTACGCAGCAACAGTCGGCGGTTTATGCCGTCCCAGGCTGATGAAGAGGCACATCAATTGTCGTATCTGCAAAAGCACTTGGCTAACATTGTGTCTC
|||| || ||| || | | | | || | || || || || | | | | | ||| | | | | || | | |||||||| || || |||||||| || ||||||||||| || | | | |||||||| || |||||||| |||||||||||||||||| | || || ||| | ||||
attttaccgataattgttctcattactgtttctatcatatgggtagagacatccttgtagctgttgagtttaa-gttaaatttcct-ttcatcatcttgcagCTTGTTCGTAGCAACAGCCGTCGGTTTATGCCATCACCGACAGATGAAGAAGCTCATCAATTATCGTATCTGCAAAAGCACATTGCAAATATTATTTCTC
upper sequence: GLYMA03G29860.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G57890.1 (Arabidopsis thaliana), 3'ss of exon 1
atttatttattattagctggtgatcggtgctttttcattcgtta---tgattctatttc--tgtttcctattctgttgttgat-tctgatgttaaatgttt-tgcagCTCGTACGCAGCAACAGTCGGCGGTTTATGCCGTCCCAGGCTGATGAAGAGGCACATCAATTGTCGTATCTGCAAAAGCACTTGGCTAACATTGTGTCTC
| | || |||| || | ||| |||| | || | | || || | | |||| || || ||| | || | ||| ||||||| || ||||||||||| || || |||||||| || ||||| ||||| || || ||||| ||||| ||||||||||| || || || ||||| | ||||
-------cactgttctttggtattctatcgtttctcatcacatgggtcgaaccaactttattggagctaaaattgttatttatatctccttttcatcatttctgcagCTTGTTCGCAGCAACAGCCGTCGATTTATGCCATCACAGGCAGATGATGAAGCTCATCAGTTGTCATATCTGCAAAAACATTTAGCAAACATCATTTCTC
upper sequence: GLYMA03G29860.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g06190.t01 (Vitis vinifera), 3'ss of exon 1
--------atttatttattattagctggtgatcggtgctttttcattcgttatgattctatttctgtttcctattctgttgttgattctgatgttaaatgttttgcagCTCGTACGCAGCAACAGTCGGCGGTTTATGCCGTCCCAGGCTGATGAAGAGGCACATCAATTGTCGTATCTGCAAAAGCACTTGGCTAACATTGTGTCTC
| |||| ||||| || | | | ||| ||| ||||| || | || || || | || | | | | |||||||| || ||||||||||| ||| |||||||||| || || || ||||||||||| |||||||| || ||| | |||||||||||||||||||| | || |
ctaacaattctgatttcttatttat--gtagttgatacttaa--attttttatg-ttgtgttgtcaaa--ctgaacttacccttatctcggt-tcgatcaaattgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAGGCTCATCAATTATCCTATTTACAAAAGCACTTGGCTAACATCCTTTCACMapped 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|19348395|gb|BM892927.1|BM892927EST: CTTCCACCTCCGCCTTCGACGGCTACTTGTCCGCTCTCTCGCCGCTTCAG CTCGTACGCAGCAACAGTCGGCGGTTTATGCCGTCCCAGGCTGATGAAGAG
genomic: CTTCCACCTCCGCCTTCGACGGCTACTTGTCCGCTCTCTCGCCGCTTCAGgtgaattctt ... tgttttgcagCTCGTACGCAGCAACAGTCGGCGGTTTATGCCGTCCCAGGCTGATGAAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattctatttctgtttcctattctgttgttgattctgatgttaaatgttttgcagCTCGTACGCAGCAACAGTCGGCGGTTTATGCCGTCCCAGGCTGATGAAGAGGCACATCAATTGTCGTATCTGCAAAAGCACTTGGCTAACATTGTGTCTC
ttctgat putative branch site (score: 3)
atgttaaatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttatttattattagctggtgatcggtgctttttcattcgttatgattctatttctgtttcctattctgttgttgattctgatgttaaatgttttgcagCTCGTACGCAGCAACAGTCGGCGGTTTATGCCGTCCCAGGCTGATGAAGAGGCACATCAATTGTCGTATCTGCAAAAGCACTTGGCTAACATTGTGTCTC
- - - - - - - -gctggtg
- - - - - - - - - - - - -ggtgctt
- - - - - - - - - - - - - - - - -ttcattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgatg