Sequence
atgc intronic sequence ATGC exonic sequenceTTTTGGGGAAGTGGTAGCTGTAACAGGTGATGGAACTAATGATGCCCCAGCACTTCATGAAGCTGACATTGGACTTGCAATGGGCATTGCTGGAACTGAGgtgagtgcaatactataatatgtttccctttgtgctgctacattttagtcatttaactcttaattttctactgcaagctaatttctcaatgtatgttcag
Basic information
species | Glycine max |
transcript | GLYMA01G40130.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G40130.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g10640.1 (Oryza sativa), 5'ss of exon 4
TTTTGGGGAAGTGGTAGCTGTAACAGGTGATGGAACTAATGATGCCCCAGCACTTCATGAAGCTGACATTGGACTTGCAATGGGCATTGCTGGAACTGAGgtgagtgcaatactataatatgtttccctttgtgctgctacattttagtcatttaactcttaattttc--tactgcaagctaatttctcaatgtatgttcag---
||||| ||||| || || || || |||||||| || |||||||| || || |||||||||||||| ||||||||||||||||||||||||||||||||||||| | | || || || || ||| | || | | || ||| | | | || | ||| | | | ||| | ||||| ||
TTTTGATGAAGTTGTTGCGGTTACTGGTGATGGCACAAATGATGCTCCTGCTCTTCATGAAGCTGATATTGGACTTGCAATGGGCATTGCTGGAACTGAGgtgattt---tcctcaaagatagttgatagtgttcccct-tgcatgaacaatataattaatgaattgcatcacttcgatttt-tttagaagtgtatttttgtggc
upper sequence: GLYMA01G40130.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G006977_T01 (Zea mays), 5'ss of exon 4
TTTTGGGGAAGTGGTAGCTGTAACAGGTGATGGAACTAATGATGCCCCAGCACTTCATGAAGCTGACATTGGACTTGCAATGGGCATTGCTGGAACTGAGgtgagtgcaatactataat-atgtttccctttgtgctgctacattttagtcatttaactcttaattttctactgcaagctaat--ttctcaatgtatgttcag-
| ||||| || ||||| || ||||| ||||| || ||||| || || |||||||| ||||| ||||| ||||||||||||||||||||||| ||||| | | | | | | | | ||||||| | ||| | | || || | | | | || ||| | || | | ||| | || | |
ACTCTACGAAGTTGTGGCTGTGACTGGTGACGGAACAAACGATGCACCTGCTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAGgtaatttcgagattttccttatgtttctaaaaataactagccatgtcattc---caattatcacactactgctgatatcttgtagtaatcaccg-atatcaaac
upper sequence: GLYMA01G40130.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G317270_T01 (Zea mays), 5'ss of exon 2
TTTTGGGGAAGTGGTAGCTGTAACAGGTGATGGAACTAATGATGCCCCAGCACTTCATGAAGCTGACATTGGACTTGCAATGGGCATTGCTGGAACTGAGgtgagtgcaatactataatatgtttccctttgtgctgctacattt--tagtcatttaactctta-attttctactgcaagctaatttctcaatgtatgttcag--
|||| ||||| || || || || || ||||| || || ||||| || || || || ||||| |||||||| ||||| |||||||||||||| |||||||| || | ||| | || | | || | || || | || || | |||| |||| | ||| | | | | | | | | ||||
GTTTGACGAAGTTGTCGCGGTGACCGGCGATGGCACGAACGATGCACCCGCGCTACACGAAGCCGACATTGGGCTTGCGATGGGCATTGCTGGCACTGAGgtacgtacg-tac-actattcactccaattcattctcgtagacttattacactattaattcttctgatgtctgtttctaatgtttgtttgtttttttgtttgaag
upper sequence: GLYMA01G40130.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G118919_T01 (Zea mays), 5'ss of exon 2
TTTTGGGGAAGTGGTAGCTGTAACAGGTGATGGAACTAATGATGCCCCAGCACTTCATGAAGCTGACATTGGACTTGCAATGGGCATTGCTGGAACTGAGgtgagtgcaatactataatatgtttccctttgtgctgctacattttagtcatttaactcttaattttctactgcaag--ctaatttctcaatgtatgttcag----
|||| ||||| || || || || || ||||| || || ||||| || || || || ||||| |||||||| ||||| |||||||||||||| |||||||| | || ||| |||| | | | || | || | ||| || | | || | || ||| | || | ||||
ATTTGATGAAGTTGTTGCGGTCACCGGCGATGGCACAAACGATGCTCCTGCGCTACACGAAGCCGACATTGGGCTTGCGATGGGCATTGCTGGCACTGAGgta----ctat-ctacttcgtgttcctaatgacgacattagacattgga-attgctcttacatataactgtggtcagtattaagtgtacatcagagtatcagacta
upper sequence: GLYMA01G40130.1 (Glycine max), 5'ss of exon 4
lower sequence: AT4G37640.1 (Arabidopsis thaliana), 5'ss of exon 4
TTTTGGGGAAGTGGTAGCTGTAACAGGTGATGGAACTAATGATGCCCCAGCACTTCATGAAGCTGACATTGGACTTGCAATGGGCATTGCTGGAACTGAGgtgagtgcaatactataatatgtttccctttgtgctgctacattttagtcatttaactcttaattttcta-ctgcaagctaatttctcaatgtatgttcag
|||| ||||| || ||||| || || |||||||| |||||||| || ||||||||||||||||| |||||||| |||||||| |||||||||||||| |||||| ||| |||| || || | | || | | | | || ||| || |||||| ||| | ||| | | |
GTTTGATGAAGTTGTTGCTGTCACTGGAGATGGAACAAATGATGCACCTGCACTTCATGAAGCTGATATTGGACTAGCAATGGGAATTGCTGGAACTGAAgtgagt---atatgataagattttgttatgtcatttgtgagagctaaagaatctaa-----aagtttctatctgta---taaccttttag-----------
upper sequence: GLYMA01G40130.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv07s0129g00180.t01 (Vitis vinifera), 5'ss of exon 4
TTTTGGGGAAGTGGTAGCTGTAACAGGTGATGGAACTAATGATGCCCCAGCACTTCATGAAGCTGACATTGGACTTGCAATGGGCATTGCTGGAACTGAGgtgagtgcaatac------tataatatgtttccctttgtgctgctacattttagtcatttaactcttaattttctactgcaagctaatttctca-atgtatgttcag
||||| ||||| || ||||| || ||||||||||| |||||||| |||||||||||||| || || ||||| || |||||||||||||||||||||||||| |||| | || ||||| ||| |||||| || | | | | | | | || | ||||| || | | | |||||
ATTTGGTGAAGTTGTTGCTGTGACCGGTGATGGAACAAATGATGCACCAGCACTTCATGAGGCAGATATTGGGCTAGCAATGGGCATTGCTGGAACTGAGgtaagtgtattatgcctttcctaatacagcattgactgtactgctaa--ttgaaaaaataggcacgtg--tacctgcaatgagctagttgataagacttatgtg---Mapped 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|16279562|gb|BI943500.1|BI943500EST: CACTTCATGAAGCTGACATTGGACTTGCAATGGGCATTGCTGGAACTGAG GTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACG
genomic: CACTTCATGAAGCTGACATTGGACTTGCAATGGGCATTGCTGGAACTGAGgtgagtgcaa ... gtatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTTTGGGGAAGTGGTAGCTGTAACAGGTGATGGAACTAATGATGCCCCAGCACTTCATGAAGCTGACATTGGACTTGCAATGGGCATTGCTGGAACTGAGgtgagtgcaatactataatatgtttccctttgtgctgctacattttagtcatttaactcttaattttctactgcaagctaatttctcaatgtatgttcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA