Sequence
atgc intronic sequence ATGC exonic sequence...ggcctatgtttagtatattgtcaaacatgttgtcttgagggttttgttttttattaatggcatgttcttatccccttttcatgtatttgatattttttagGACATTGGAGGATGTGATATCCAGAAACAGGAAATCCGCGAGGCCGTGGAGCTACCCCTTACGCATCATGAACTATACAAACAAATTGGTATTGATCCTC
Basic information
species | Glycine max |
transcript | GLYMA11G31450.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 1
ggcctatgtttagtatattgtcaaacatgttgtcttgagggttttgttttttattaatggcatgttcttatccccttttcatgtatttgatattttttagGACATTGGAGGATGTGATATCCAGAAACAGGAAATCCGCGAGGCCGTGGAGCTACCCCTTACGCATCATGAACTATACAAACAAATTGGTATTGATCCTC
| || | | | || | | || || | | | | | | | | |||| || | ||| |||| |||| |||||||||||||| ||||| ||||| ||||| || ||||| || || |||| || || |||||||| || ||||| || ||||||||||||||||
ctcacatatcctggagcttatttattattgctcactgtaatctattcatacagtcgacaaataaaatatttaacatttttttgcttctgactattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAATTACCGCTGACACATCATGAGCTGTACAAGCAGATTGGTATTGATCCTC
upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 1
ggcctatgtttagtatattgtcaaacatgttgtcttgagggttttgttttttattaatggcatgttcttatccccttttcatgtatttgatattttttagGACATTGGAGGATGTGATATCCAGAAACAGGAAATCCGCGAGGCCGTGGAGCTACCCCTTACGCATCATGAACTATACAAACAAATTGGTATTGATCCTC
| ||| || ||| | | | |||| | | | | ||| | || ||| || || | | || | | |||| ||||||||||| || ||||| || || ||||| || ||||| || ||| ||||| | || |||||||| | ||||| || ||||||||||||||||
ttctaatggtttgtaaggaattggctctaatttctttaagtacacctatgcatttagtatcagtgcattacaattttcattggtttcttatggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAGTTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC
upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 1
--ggcctatgtttagtatattgtcaaacatgttgtcttgagggttttgttttttattaatggcatgttcttatccccttttcatgtatttgatattttttagGACATTGGAGGATGTGATATCCAGAAACAGGAAATCCGCGAGGCCGTGGAGCTACCCCTTACGCATCATGAACTATACAAACAAATTGGTATTGATCCTC
| || | |||| | | | || ||| | | | ||| | || ||| | || || ||| || | | |||| |||||||||||||| ||||| || || ||||| || ||||| || || ||||| | || |||||||| | ||||| || ||||||||||||||||
ttctctagtggcttgtatggatttggctctaatttcatgaagtgcacctatgcctttagtttcagtgcattacaatttattg--gttttttatggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAATTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC
upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 3'ss of exon 1
--------ggcctatgtttagtatattgtcaaacatgttgtcttgagggttttgttttttattaatggcatgttcttatccccttttcatgtatttgatattttttagGACATTGGAGGATGTGATATCCAGAAACAGGAAATCCGCGAGGCCGTGGAGCTACCCCTTACGCATCATGAACTATACAAACAAATTGGTATTGATCCTC
| | | | |||||| ||||| || ||| | |||| | || | | | | | || |||| |||| | ||| |||||| ||||||||||||||||| ||||| ||||||||||| || || || ||| |||| | || |||||||| || |||||||| |||||||| |||||||
tatttgaatgtttgccatctttttattgt-aaacacatt-tctaaatggttggggttctggtcagagtttgaaattcatggtttttt--tgtacct----tttattagGATATTGGAGGATGTGATATTCAGAAGCAGGAAATCCGTGAAGCTGTTGAGTTACCTTTGACTCATCATGAGCTGTACAAACAGATTGGTATAGATCCTC
upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S147_100V6.1 (Physcomitrella patens), 3'ss of exon 1
ggcctatgtttagtatattgtca--aacatgttgtcttgagggttttgttttttattaatggcatgttcttatccccttttcatgt-atttgatattt--tttagGACATTGGAGGATGTGATATCCAGAAACAGGAAATCCGCGAGGCCGTGGAGCTACCCCTTACGCATCATGAACTATACAAACAAATTGGTATTGATCCTC
| | | || || || || |||||| | | | || || ||| | || | || | || | | | ||| || | | | |||| ||||| ||||| ||||| |||||||| |||||| | || || |||||||| || ||||| ||||| || |||| || || ||||||||||| || |
-----aaggcttgttcatctgcatgaatctgttgttataatgtttgcaattcttacgagtgcagttttttaatactttcatattgtcgaatggtggtggatgcagGATATTGGTGGATGCGATATTCAGAAACAAGAAATCAGGGAAGCTGTGGAGCTTCCACTTACACATCACGAGTTATATAAGCAGATTGGTATTGACCCAC
upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S36_183V6.1 (Physcomitrella patens), 3'ss of exon 1
ggcctatgtttagtatattgtcaaacatgttgtcttgagggttttgttttttattaatgg--catgttcttatccccttttcat-gtatttgatattttt-----tagGACATTGGAGGATGTGATATCCAGAAACAGGAAATCCGCGAGGCCGTGGAGCTACCCCTTACGCATCATGAACTATACAAACAAATTGGTATTGATCCTC
| || | || || || || | ||| || ||||| | | || ||| | | |||| | || | || | |||| ||||| ||||||||||| || ||||| || || | |||||||||||||| || ||||| ||||||||||||||||| || ||||| || || || |
--------agaaaaatgatttccgttatagggttacgaagcagatgtcttagtttaattgttcccatttatatgcattgttcaaagcgattcgtgttcgtgagtgcagGATATTGGTGGATGTGATATACAAAAACAAGAGATTAGAGAGGCCGTGGAGCTTCCACTTACACATCATGAACTATACAAGCAGATTGGCATCGACCCAC
upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ04233 (Selaginella moellendorffii), 3'ss of exon 1
ggcctatgtttagtatattgtcaaacatgttgtcttgagggttttgttttttattaatggcatgttcttatccccttttcatgtatttgatattttttagGACATTGGAGGATGTGATATCCAGAAACAGGAAATCCGCGAGGCCGTGGAGCTACCCCTTACGCATCATGAACTATACAAACAAATTGGTATTGATCCTC
|| || || || | | || | | | | | || | || | | ||| |||| |||||||| ||||| |||||||| || ||||||||||||||||||||||| || || ||||| || || |||||||| || |||||||| ||||| |
--------------------gtaagaatttttctttcttcttgcgactcttgagggctcgtgttcttgggtctaagcacttctttctttgtttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTATACAAGCAGATTGGTATCGATCCAC
upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ38338 (Selaginella moellendorffii), 3'ss of exon 1
ggcctatgtttagtatattgtcaaacatgttgtcttgagggttttgttttttattaatggcatgttcttatccccttttcatgtatttgatattttttagGACATTGGAGGATGTGATATCCAGAAACAGGAAATCCGCGAGGCCGTGGAGCTACCCCTTACGCATCATGAACTATACAAACAAATTGGTATTGATCCTC
|| | || |||| | || | || | | | | | || || || | | ||| |||| |||||||| ||||| |||||||| || ||||||||||||||||||||||| || || ||||| || || || ||||| || |||||||| ||||| |
---------------------gtaagaaattttctt-----tcttactcttgaaggctcgtgttcttgggtctaaacacttcttactttgtttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTTTACAAGCAGATTGGTATCGATCCACMapped 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|6069862|gb|AW099462.1|AW099462EST: NCAGCATCTCGCTCCTCAGCCAGTCCGAGAAGCCTGACGTCACTTATAAT GACATTGGNAG-ATGTGATATCCAGAAACAGGANATCCGCCGAG-CCGTGG
genomic: CCAGCATCTCGCTCCTCAGCCAGTCCGAGAAGCCTGACGTCACTTATAATgtcagtttct ... tattttttagGACATTGG-AGGATGTGATATCCAGAAACAGGAAATCCGC-GAGGCCGTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttttattaatggcatgttcttatccccttttcatgtatttgatattttttagGACATTGGAGGATGTGATATCCAGAAACAGGAAATCCGCGAGGCCGTGGAGCTACCCCTTACGCATCATGAACTATACAAACAAATTGGTATTGATCCTC
tatttttt CT-rich tract
ttttcatgtatttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggcctatgtttagtatattgtcaaacatgttgtcttgagggttttgttttttattaatggcatgttcttatccccttttcatgtatttgatattttttagGACATTGGAGGATGTGATATCCAGAAACAGGAAATCCGCGAGGCCGTGGAGCTACCCCTTACGCATCATGAACTATACAAACAAATTGGTATTGATCCTC
- cctatgt
- - - - - - - - - - -caaacat
- - - - - - - - - - - - - - - tgtcttg
- - - - - - - - - - - - - - - - - - - -ggttttg