Sequence
atgc intronic sequence ATGC exonic sequencegtaagacttactcaagttgttgatttttgacaatttgatttgatgggatcaatggtgactgacatgtatccttttgcagGTTTGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTTAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT
Basic information
species | Glycine max |
transcript | GLYMA05G36600.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 2
---gtaagactt-actcaag--ttgttgatttttgacaatttgatttgatgggatcaatggtgactgacatgtatccttttgcagGTTTGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTTAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT
| |||| || | | | | | | ||| | | | || | |||| || | | ||||||||||||||| ||||||||||| || || ||||| ||||| || || |||||||| |||||||| || || || ||||| ||||| || || ||||||||
gtaatggcactttaccctatgctcgctcttatttcctgttgttgatcactgctgcctgatctgacctgtataattattcttgcagGTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGATTGTGAACAAGGACGGTAAGCCCTACATTCAGGTCAAGATCAAGGATGGA
upper sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 2
gtaa-gacttactcaagttgttgatttttgacaatttgatttgatg-ggatcaa---tggtgactgacatgtat--ccttttgc--agGTTTGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTTAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT
||| | || ||| ||| || | | || | | | || || | | ||| | || || |||| || |||| |||||| | ||||||||||| || || || ||||| ||||| || || |||||| ||||||||||||| || || ||||| ||||| || || ||||||||
gtagtgcctctctcccacaattg-cttctattatttcgtctcgctgtgggttatgtctggcgtcttacctgtaatgcccattgcttagGTTTCAGGATAAGGAAGTCCAGAGGGACATGAAACTTGTCCCCTACAAGATTATTAACAAGGATGGCAAGCCATACATTCAGGTCAAGATCAAGGATGGG
upper sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 2
gtaagactta-ctcaagttgttgatttttgacaatttgatttgat---ggg--atcaatggtgactgacatgta-------tccttttgc--agGTTTGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTTAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT
|||| || | ||| ||| || | ||||| | | | ||| || ||| | || | | || || ||| ||||| | || |||||||| || || || ||||| |||||||| || |||||| ||||||||||||| || || ||||| ||||| || || ||||||||
gtaacacctctctcctacagttacttctgttgaatttcgtctcgttgtgggttatttctggcgtcttaactttagtaatgccccatttatttagGTTCGCGGACAAGGAAGTCCAGAGGGACATGAAACTTGTTCCCTACAAGATTATTAACAAGGATGGCAAGCCCTACATTCAGGTCAAGATCAAGGATGGG
upper sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagacttactcaagttgttgatttttgacaatttgatttgatgggatcaatggt----gactgacatgtatccttttgcagGTTTGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTTAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT
| ||||| | | | ||| | || ||| |||| || |||| | || | | ||| |||| ||||| |||||||| ||||||| |||| ||| ||||| ||||| ||||||| ||||||||||| || || ||||| || || || || |||||||||
---gtaattacttattctctgtgtttgtttcaccttgga--gatgatattgttggtttaagtctttgttattgtatttggcagATTTGAGGATAAGGAGGTTCAAAAGGATAGGAAACTTGTACCTTACCAGATTGTGAACAAGGATGGTAAGCCATACATTCAAGTCAAGATCAAGGATGGT
upper sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 2
-------gtaagacttactcaagttgttgatttttg-acaatttgatttgatggga---tcaatggtgactgacatgtatccttttg-cagGTTTGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTTAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT
|| || || ||| | ||| | | || | | | | ||| | | || ||| | |||||| |||||||||||||||||| ||||| | || |||||||||||||| || || ||||||||||||||||| || |||||||| || || || || |||||||||
gtaatacgtctatctatctaaagcttttggtctatgcattgtattagttggcaaggaactttttgctgaggcttttaatcacttttgacagGTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAACATTGTTAACAAGGATGGGAAGCCTTACATTCAAGTCAAGATCAAGGATGGT
upper sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ17607 (Selaginella moellendorffii), 3'ss of exon 2
gtaagacttactcaagttgttgatttttgacaatttgatttgatgggatcaatggtgactgacatgtatccttttgcagGTTTGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTTAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT
||||| | || || |||||| | | ||| | |||| | || | | | |||||||||||| || || ||||||| |||||||||||| |||| | |||||| || ||||||||||||||||| ||||| || || || | ||||||||
gtaagttagattcccatttgcaatttttc-ctacttgttccttcttgatc---------taactctcgtaccgtcacagGTTTGAAGACAAAGAGGTTCAAAAAGATATGAAGCTCTTTCCATTTAAGATCGTCAACAAGGATGGAAAACCGTACATCCAAGTCAAGGTGAAGGATGGC
upper sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 2
gtaagacttactcaagttgttgatttttgacaatttgatttgatgggatcaatggtgactgacatgtatccttttgcagGTTTGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTTAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT
||||| | || || |||||| | | ||||| || || | | | ||||||||||| || || |||||||||||||||||||| |||| | |||||| || ||||||||||||||||| ||||| || || || | ||||||||
gtaagttagattcccatttgcaattttt--ccttccttcttgat--------------ctaactctcgtaccgtcatagGTTTGAAGACAAAGAGGTTCAAAGAGATATGAAGCTCTTTCCATTTAAGATCGTCAACAAGGATGGAAAACCATACATCCAAGTCAAGGTGAAGGATGGCMapped 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|16276964|gb|BI942132.1|BI942132EST: GTCAATCCAGAAAGGACCATCTTTGATGTCAAGAGACTTATTGGAAGAAA GTTTGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGAT
genomic: GTCAATCCAGAAAGGACCATCTTTGATGTCAAGAGACTTATTGGAAGAAAgtaagactta ... ccttttgcagGTTTGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGAT
EST:
gi|151402800|gb|EV272613.1|EV272613EST: GTCAATCCAGAAAGGACCATCTTTGATGTCAAGAGACTTATTGGAAGAAA GTTTGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGAT
genomic: GTCAATCCAGAAAGGACCATCTTTGATGTCAAGAGACTTATTGGAAGAAAgtaagactta ... ccttttgcagGTTTGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgacaatttgatttgatgggatcaatggtgactgacatgtatccttttgcagGTTTGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTTAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT
gactgac putative branch site (score: 2)
tatcctttt putative PPT
aatttgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagacttactcaagttgttgatttttgacaatttgatttgatgggatcaatggtgactgacatgtatccttttgcagGTTTGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTTAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG