Sequence
atgc intronic sequence ATGC exonic sequence...gactataaactgactatcagcttgctggtatttatccaataattaggtgttgttaccgtgacagaatattgagggagggagcatttcaattgtcttgcagGAACCACATGTGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAATCGCGGCTGGAATGAATGCAATGGACCTGAGGCGGGGTATAAG
Basic information
species | Glycine max |
transcript | GLYMA20G19980.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 3
---------gactataaactgactatcagcttgctggtatttatccaataattaggtgttgttaccgtgacagaatattgagggagggagcatttcaattgtcttgcagGAACCACATGTGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAATCGCGGCTGGAATGAATGCAATGGACCTGAGGCGGGGTATAAG
| ||||||| ||| ||| || | ||| || | ||||| | | | ||| | | || || || | |||| |||||||||||||| || | ||| ||||||||||||||| || |||||||| | ||||||||||||||||||||||| | ||||| || ||
tgaccggtctaacataaactatgcctcatattgttgaattgtat---gtagct---tgttgatgctttcttcgaactgtacgtgatctgatatccaaaaaatt---cagGTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCAAATCTGTTGCGGCTGGAATGAATGCAATGGATTTAAGGCGTGGAATCTC
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 3
----gactataaactgactatcagcttgctggtatttatccaataattaggt-gttgttaccgtgacagaatattgagggagggagcatttcaattgtcttgcagGAACCACATGTGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAATCGCGGCTGGAATGAATGCAATGGACCTGAGGCGGGGTATAAG
| || | | | | | || ||||| || ||| | | || | | | || | || ||| || || |||| ||||||||||| || || | ||| ||||||||||||||| || |||||||| | ||||||||||||||||||||||| | ||||| || ||
attgaatcatgtaataa--gttaaattttctatatttgaattgtatgtagcttgctgatgtcttcttccaactgtacctgatctgacatccaaaaa---tttcagGTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCAAATCTGTTGCGGCTGGAATGAATGCAATGGATTTAAGGCGCGGAATCTC
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 4
---------gactataaactgactatcagcttgctggtatttatccaataattaggt-gttgttaccgtgacaga--atattga--gg-------------gagggagcatttcaattgtcttgcagGAACCACATGTGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAATCGCGGCTGGAATGAATGCAATGGACCTGAGGCGGGGTATAAG
|| | || || || | || | | ||| | | ||||| ||| ||| | | | | ||||| | || || | || | || || ||||||| || ||||| ||||||||||| |||| || || || ||||| || |||||| | || ||||||||||||||||||||||| || || ||||| |
gtaagtgttccctttcaatggattaaaacgttttttctgtttttgc--taattgggttgttagtctcctatctactcatattaatcggtgtttttgtatctgacaaaatatatggtatgcgttacagGAACAACGTGTGCCACAGTCCTTACTAGAGCTATCTTCACGGAAGGTTGTAAATCAGTTGCCGCTGGAATGAATGCAATGGACCTAAGACGTGGTATCAA
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 3
gactataaactgactatcagcttgctggtatttatccaataattaggtgttgttaccgtgacagaatattgagggagggagcatttcaattgtcttgcagGAACCACATGTGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAATCGCGGCTGGAATGAATGCAATGGACCTGAGGCGGGGTATAAG
||| | | ||| ||| | | |||| | | ||| ||| | || || || || || | | ||| | ||||| |||||| || || |||||||| ||||| || || || |||||| | ||||| ||||||||| | || || |||||||||||||||||| || | | |||||
----gtaagata--tttcattttgat--tgattatgcggttcatagttgtagaaactttg-caaaactatgtaccaatgcttgtttaacttgtcatgcagGTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAAGGATGCAAATCAGTTGCCGCAGGAATGAATGCAATGGACTTGCGAAGAGGTATTTC
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------------------------------------------------------------------gactataaactgactatcagcttgctggtatttatccaa--taattaggtgttgttaccgtgacagaatattgagggagggagcatttcaattgtcttgcagGAACCACATGTGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAATCGCGGCTGGAATGAATGCAATGGACCTGAGGCGGGGTATAAG
||| | | | | | | | || | | | || | ||| | | ||| | || | || | | || | |||||||||||| ||| ||||| || |||||||| || ||| ||||||| ||||||||| | || ||||| ||||| ||||||||| || | |||| || |
gcaagtgctctgtgtcatataatttgtgaagtttgagttcttagtcaggagcattattttcttgaatattgcagggtctaccgtattcaatctaatgacgacacatttag-acgtgattatagacactgttcgtggttgtttaactatccgattcgtactgggatcatttggctaacattggctgaaacaccctgcagGAACCACTGCTGCAACAGTGCTCACACGAGCTATTTTTGCTGAAGGGTGCAAATCAGTAGCAGCTGGTATGAACGCAATGGACTTGCGCAGGGGCATCAA
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------------------------------gactataaactgactatcagct-tgctggtatttatccaataattaggtgttgttaccgtgacagaatattgagggagggagcatttcaattgtcttgcagGAACCACATGTGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAATCGCGGCTGGAATGAATGCAATGGACCTGAGGCGGGGTATAAG
|| || || || || | |||| || | ||| | || ||| ||| ||| | || | | || | | |||| |||||||||| || ||||| ||||| || || |||||||| ||| ||| |||||||||||| | || ||||| ||||| ||||||||||| | | ||||| ||
gtatatgcctaatcccagttgactgtgtgaacctcgttctgatgcatgatttcaacctactttttcattttgtatgaatctatggaatactcttatacagattaacatcagcactggc-cttgccaaatcaataaatgtatctacagtgcaatgatttcactgactcgaagttatgaatt---ttgcagGAACAACTTGTGCAACAGTGCTCACCCGAGCAATTTTTGTTGAGGGCTGCAAATCAGTTGCAGCTGGCATGAACGCAATGGACCTACGTAGAGGTATTAGMapped 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|19269094|gb|BM885350.1|BM885350EST: CAGTCTTGTAAAGCAGGTTGCTAATGCTACTAATGATGTGGCTGGTGATG GAACCACATGTGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCA
genomic: CAGTCTTGTAAAGCAGGTTGCTAATGCTACTAATGATGTGGCTGGTGATGgtaagctgat ... tgtcttgcagGAACCACATGTGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtgttgttaccgtgacagaatattgagggagggagcatttcaattgtcttgcagGAACCACATGTGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAATCGCGGCTGGAATGAATGCAATGGACCTGAGGCGGGGTATAAG
ttgtctt CT-rich tract
atttcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gactataaactgactatcagcttgctggtatttatccaataattaggtgttgttaccgtgacagaatattgagggagggagcatttcaattgtcttgcagGAACCACATGTGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAATCGCGGCTGGAATGAATGCAATGGACCTGAGGCGGGGTATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - -ctgacta
- - - - - - - - - -gcttgct
- - - - - - - - - - - - - - - - - - - - - - -ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - -taccgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggaggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatttc