Sequence
atgc intronic sequence ATGC exonic sequence...tgtgccaaaatcccttaaacataatccttcaagtgctgaggtgttttctcgttcctaacagtgaatcaacctctcactatttgtctaatgtgtgttgcagGTAACCCCAGGGTAACTCCAGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATTTGTACTTCTCTCAGATTGAGGATCTCATGTT
Basic information
species | Glycine max |
transcript | GLYMA06G43050.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G43050.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 4
tgtgccaaaatcccttaaacataatccttcaagtgctgaggtgttttctcgttcctaacagtgaatcaacctctcactatttgtctaatgtgtgttgcagGTAACCCCAGGGTAACTCCAGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATTTGTACTTCTCTCAGATTGAGGATCTCATGTT
| || || | || | | ||| | | | |||| | | | || | | ||| | ||| | ||| || || || || || |||||||| ||||||||||| || ||||| ||||||||||||||| | ||||| |||| ||| || |||||||||||||||||
---------gtatgcaaaggatgg-cttttgacttctg---tatagttcagttcttgtgcatttaataattttgtgc-attgcaccaattt-------agGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTAGAATGATGGCTTCAAATTTATACTGCTCGCAAATTGAGGATCTCATGTT
upper sequence: GLYMA06G43050.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g14670.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------tgtgcc---aaaatcccttaaacataatccttcaagtgctgaggt-gttttctcgttcctaacagt-----gaatcaacctct-------cactatttgtctaatgtgtgttgcagGTAACCCCAGGGTAACTCCAGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATTTGTACTTCTCTCAGATTGAGGATCTCATGTT
| |||| |||| | | || ||| || | || || || || || ||| || | || | | ||| | ||| | || |||| || |||| || || || || || ||||| |||||||||||||| || ||||| || ||||||||||| || || ||||| | ||| || |||||||||||||||||
gtgagaaacatatctattttgttgttggttcttagcactatgccttataaataattacagcacaatgaatcctctttagatgttgtctttaaattactaccacttaggagataccatgtctgtatgcactctaaatttcaaatgacctttacagGAAATCCAAGAGTCACACCAGAGGTTACAAGGGATGTCTGCTTGCTTGCAAGAATGATGGCAGCAAACTTGTATTGCTCACAAATTGAGGATCTCATGTT
upper sequence: GLYMA06G43050.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
-----------tgtgccaaaatcccttaaacataatccttcaagtgctgaggtgtt---ttctcgttcctaacagtgaatcaacctctcactatttgtctaatgtgtgttgcagGTAACCCCAGGGTAACTCCAGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATTTGTACTTCTCTCAGATTGAGGATCTCATGTT
| | | | || | | || || | ||||||| | | | |||| || | ||| | | || |||| | |||| || || || || || ||||| |||||||||||||| || ||| |||||||||||||||||||||||||||| | ||||| || || || |||||
gtacatagcattctctctcccttatttggatagtatatttgatgtgctgaatcatgcaactgtagttcacaagaaagaagtgcaaatataactctgaactgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
upper sequence: GLYMA06G43050.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------tgtgccaaaatcccttaaacataatccttcaagtgct----gaggtgttttctcgttcc-----taacagtgaatca-acctct-cactattt--gtctaatgtgtgt-----tgcagGTAACCCCAGGGTAACTCCAGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATTTGTACTTCTCTCAGATTGAGGATCTCATGTT
| ||| | | | ||| | ||| |||| | || || || || || | | | | | |||||| ||||| ||||| | | |||||| || || || || || ||||| ||||| |||||||| || ||||| || ||||||||||| | || ||||||| ||||||||||||||||||||||||
gtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcagtatttgc-agcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtctctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTTMapped 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|26045705|gb|CA783206.1|CA783206EST: TAATGCCCCTGTTATTCAATTCTCTTCTTGGATGGGAGGAGATCGTGATG GTAACCCCAGGGTAACTCCAGAAGTTACAAGGGATGTGTGTTTGCTGGCTA
genomic: TAATGCCCCTGTTATTCAATTCTCTTCTTGGATGGGAGGAGATCGTGATGgtatcgttct ... tgtgttgcagGTAACCCCAGGGTAACTCCAGAAGTTACAAGGGATGTGTGTTTGCTGGCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctcgttcctaacagtgaatcaacctctcactatttgtctaatgtgtgttgcagGTAACCCCAGGGTAACTCCAGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATTTGTACTTCTCTCAGATTGAGGATCTCATGTT
actattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgccaaaatcccttaaacataatccttcaagtgctgaggtgttttctcgttcctaacagtgaatcaacctctcactatttgtctaatgtgtgttgcagGTAACCCCAGGGTAACTCCAGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATTTGTACTTCTCTCAGATTGAGGATCTCATGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- tgccaaa
- - - - - -cccttaa
- - - - - - - - - - - - - - -caagtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctcac