Sequence
atgc intronic sequence ATGC exonic sequence...atatatatatatatatatatataccaattctccatacacgatttgaagagaatgaactttttacatggtgttaactaattgatgtcttgtaacttttcagGAATGGGTGACAGATAATCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
Basic information
species | Glycine max |
transcript | GLYMA01G09660.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G09660.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 6
atatatatatatatatatatataccaattctccatacacgatttgaagagaatgaactttttacatggtgttaactaattgatgtc-ttgtaacttttcagGAATGGGTGACAGATAATCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
|| ||||||| | | | | || || || | | | || ||| | | ||||| ||||| | ||| ||| | ||| |||| |||||||| |||||||| ||| ||||||||||||| ||||| ||||| |||||||| || |||||||| || | ||||| |||||||| || ||||
-agcttagatatatactcctttgctataccttattatcatatcgtatttgcaataattttgaaatttgtgttcactaacttgtgttattgataatttgaagGAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAAGTCAGTGTTCGTCTTCTTGGAGGTTTGATGGCATTGGGATATACTATAG
upper sequence: GLYMA01G09660.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G147430_T02 (Zea mays), 3'ss of exon 6
atatatatatatatatatatataccaattctccatacacgatttgaagagaatgaactttttaca-------tggtgttaactaa-----ttgatgtcttgtaacttttcagGAATGGGTGACAGATAATCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
|| | | | ||| ||| | || | || | || ||| || ||||||| ||||| || | || | || ||||||||||||| || ||| | ||| ||||||||||||| || |||||||| |||||||| || ||||||||||| | ||||| |||||||| || ||||
-----------ctgctacttgtttctattgtccgtg-actacatgcaataaacaaacccttgctggcagccctggtgttcactaactctcttattccattctgtgttcaaagGAATGGGTGACCGACAATTCTTTTATCATATCACCAAGGATCACTTTTGAAGTCAGTGTTCGTCTTCTTGGTGGTTTGATGGCATTGGGATATACTATAG
upper sequence: GLYMA01G09660.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G26190.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------atatatatatatatata-tatataccaattctccatacacgatttgaagagaatgaactttttacatggtgttaactaattgatgtcttg---taacttttcagGAATGGGTGACAGATAATCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
|| |||| ||| | ||| | || || | | | | ||| | | | ||| || | | ||| || || || | ||||||||||| || |||| ||| ||||||||||| ||||| ||||| ||||| |||||||| ||||| |||||||| || ||||| ||||||||||||||||
gtttgttcagagtttattttccatgttctcatcaatatgactattcaatatctggaaaagctg-acaatccctctgattctggtaagatgcttagtatctggtgaataactgtggttctggttttgacaaccagGAATGGGTTACGGATACTCCTTTTGTCATATCCCCAAGGATTACATTTGAAGTCAGTGTTCGCCTACTTGGTGGGCTCATGGCATTGGGATACACAATAG
upper sequence: GLYMA01G09660.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0010g01080.t01 (Vitis vinifera), 3'ss of exon 5
atatatatatatatatata-tataccaattctccatacacgatttgaagagaatgaactttttacatggtgttaactaattgatgtcttgtaact--tttcagGAATGGGTGACAGATAATCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
| | | | | | | | | | | || | | | | ||| || |||| | | | | | | |||| ||| || |||||||||||||| || |||||||||||||| |||||||||||||| |||||||| ||||||||||| ||||||||||| |||||||| ||||| ||||||||||
acacct-tgtctttgtctggtttgttaacttcctaaggtcatttt--agtccatgagaaatacgcgagacttgcccaatctgatcagttggttctcatttcagGAATGGGTTACTGATAATCCATTTGTTATATCACCAAGAATAACTTTTGAAGTCAGTGTGCGGCTTCTTGGTGGGCTAATGGCCTTGGGGTACACAATAGMapped 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|15812935|gb|BI785210.1|BI785210EST: CATATTTACGGATGCGAAATAAAGATGGGAAATACAGTCTCATGTTTGAG GAATGGGTGACAGATAACCCATTTGTCATATCACCAAGAATTACTTTTGAG
genomic: CATATTTACGGATGCGAAATAAGGATGGGAAATACAGTCTCATGTTTGAGgtttggttcc ... aacttttcagGAATGGGTGACAGATAATCCATTTGTCATATCACCAAGAATTACTTTTGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagagaatgaactttttacatggtgttaactaattgatgtcttgtaacttttcagGAATGGGTGACAGATAATCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
ttgtaac putative branch site (score: 2)
cttttc CT-rich tract
ttaactaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatatatatatatatatatataccaattctccatacacgatttgaagagaatgaactttttacatggtgttaactaattgatgtcttgtaacttttcagGAATGGGTGACAGATAATCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - catacac
- - - - - - - - - - - - - - - - - - - - - - gaagagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtc