Sequence
atgc intronic sequence ATGC exonic sequencegtgattgtttgtgcccttttgctacttacatgtgattccagctttgcttattacaagttattctgtcgggagagttcataaacactgtattctaaatcattttgcttgctcagGATGTTGTGACAGAAAATGAATTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAGTGACATCGATGTTACTTTTGATGATATTGGAGCTCTTGAAA
Basic information
species | Glycine max |
transcript | GLYMA05G03270.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 20
gtgattgtttgtgcccttttgctacttacatgtgattccagctttgcttattacaagttattctgtcgggagagttcataaacactgtattct-aaatca-ttttgcttgctcagGATGTTGTGACAGAAAATGAATTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAGTGACATCGATGTTACTTTTGATGATATTGGAGCTCTTGAAA
| | | | || ||| ||| || | |||| | | | | | || || | ||| | || || ||| |||| | |||| | | || |||||||||| ||||| || |||||||| || |||||| |||| |||||||| ||||||| |||||| | || || ||||||||||||||||| | ||||
------------gttactctccatct--catcatattgcaaacata-ttatcatac-tcacacagttggaat--ctcacag-tgctttactcttaaattactttttccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA
upper sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 11
gtgattgtttgtgcccttttgctacttacatgtgattccagctttgcttattacaagttattctgtcgggagagttcataaacactgtattctaaatcattttgcttgctcagGATGTTGTGACAGAAAATGAATTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAGTGACATCGATGTTACTTTTGATGATATTGGAGCTCTTGAAA
||| | | | || ||||| || || |||| ||| | | || | |||||| || | || ||| | ||||||||||||| ||||| ||||||||||| || |||||||||| |||||||| ||||||| |||||| | ||||| ||||||||||||||||| | || |
---------------------gtacaatcccctacatattgccgtgctttttg---gtgattcc-tcgagttatttactgaacactctacttacaagtccttt---ttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
upper sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 5
gtgattgtttgtgcccttttgctacttacatgtgattccagctttgc--ttattacaagttattctgtcgggagagttcataaacactgtat-tctaaatcattttgcttgctcagGATGTTGTGACAGAAAATGAATTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAGTGACATCGATGTTACTTTTGATGATATTGGAGCTCTTGAAA
| | ||| ||| | | | | || |||| || | |||| | || ||| ||| | |||||| |||| || ||||||||||| ||||| ||||| ||||| || ||||||||||| |||||||| || || | |||||| | ||||| ||||||||||||||||| | || |
---------------------------gtacactctcccaatattgtcatgagttctggtgattcc-tcaagttagttgctgaatactctatgtataaatcctttttct----cagGATGTTGTCACAGAGAATGAGTTTGAGAAAAGGCTTTTGGCAGATGTTATACCTCCAAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
upper sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 20
---gtgattgt-ttgtgcccttttgctactt--acatgtgattccagctttgct--tattacaagttattctgtcgggagagttcataaacactgtattctaaatcattttgcttgc-----tcagGATGTTGTGACAGAAAATGAATTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAGTGACATCGATGTTACTTTTGATGATATTGGAGCTCTTGAAA
|| ||| | || || | || ||| || || | ||||||| | ||| | | || | | || | || | || | || | | ||||||| ||| || |||||||| ||||||||||||||| | || |||||||| || || ||| |||| |||||| ||||| || ||||||||| | ||||
gtagtcattttcttttgttatattaggactcgaacccgttaatccagctcagtctctatgttgatcttcagagttttggaaattgttttactgtatagagcttactgttctctctaacaatgtcagGATATTGCTACGGAAAATGAGTTTGAAAAGAGGCTTCTTGCAGATGTTATCCCTCCACATGAAATCGGTGTTACCTTTGAGGACATTGGAGCTTTAGAAA
upper sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 20
gtgattgtttgtgcccttttgctacttacatgtgattccagctttgcttattacaagttattctgtcgggagagttcataaacactgtattctaaatcattttgcttgctcagGATGTTGTGACAGAAAATGAATTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAGTGACATCGATGTTACTTTTGATGATATTGGAGCTCTTGAAA
| |||| ||| | |||| | | | ||| | | ||||||||| || | | || || | |||| |||| |||||||||||| ||||||||||||||||| || |||||| | ||||||||||||||||| |||||| | || || |||||||||||||| || || ||||
------------gtaatttttgtaccttcatgcaacta-atttttatctttaacaagttatattga---------ttaaaatcaatttatttccaatc-----------tcagGATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATTCCACCATCTGACATTGGGGTCACATTTGATGATATTGGGGCCCTGGAAAMapped 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|193435526|gb|FK401958.1|FK401958EST: TCTATCCAGAATGAGTCTAAGAGCCTGAAGAAATCTCTTAAG GATGTTGTGTCAGAAAATGAATTTGAAAAGAGGCTTTTGGCTGATGTTTAT
genomic: TCTATCCAGAATGAGTCTAAGAGCCTGAAGAAATCTCTTAAGgtgattgttt ... gcttgctcagGATGTTGTGACAGAAAATGAATTTGAAAAGAGGCTTTTGGCTGATG-TTAT
EST:
gi|33390647|gb|CA853842.1|CA853842EST: TCTTGCAGTCTATCCAGAATGAGTCTAAGAGCCTGAAGAAATCTCTTAAG GATGTTGTGACAGAAAATGAATTTGAAAAGAGGCTTTTGGCTGATGTTATT
genomic: TCTTGCAGTCTATCCAGAATGAGTCTAAGAGCCTGAAGAAATCTCTTAAGgtgattgttt ... gcttgctcagGATGTTGTGACAGAAAATGAATTTGAAAAGAGGCTTTTGGCTGATGTTATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattctgtcgggagagttcataaacactgtattctaaatcattttgcttgctcagGATGTTGTGACAGAAAATGAATTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAGTGACATCGATGTTACTTTTGATGATATTGGAGCTCTTGAAA
ttctaaa putative branch site (score: 2)
ttttgctt putative PPT
tattctaaatcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattgtttgtgcccttttgctacttacatgtgattccagctttgcttattacaagttattctgtcgggagagttcataaacactgtattctaaatcattttgcttgctcagGATGTTGTGACAGAAAATGAATTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAGTGACATCGATGTTACTTTTGATGATATTGGAGCTCTTGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT