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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttctattggtttcacaattttaactggtatctgttgctttgcattggatttgcagcactttccttgttgtgttattgtaaaccattattcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG

Basic information

species Glycine max
transcript GLYMA05G37850.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G37850.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 3'ss of exon 11
gttagtttctattggtttcacaattttaactggtatctgttgctttgcattggatttgcagcactttccttgttgtgttattgtaaaccattattc--ttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG
|| | ||||| | | | | ||| || | ||| | | | |||| |||| || ||||||||||||||| | ||| | |||||||||||||||||||| || || ||||| |||||||||||||| ||||||||||||
----------gtttgcccttaaatttgtatagctgatcatcatggcatgttgacactgtaa-gcttaatgtaataactatttgttcttttgtatttggcttgcagGTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGG

upper sequence: GLYMA05G37850.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 11
gttagt--ttctattggtttcacaattttaac-tggtatctgttgctttgcattggatttgcagcactttccttgttgtgttattgtaaaccattattcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG
||| | ||| ||| || | || | | | ||| || | | | || || || | | | | | |||| | ||||| | | || ||||| ||||||||| | ||| | |||||||||||||||||||| || || ||||| |||||||||||||| |||| |||||||
gtttgcccttcaatttgtatagcacgatcatcatggcatgt-tgacactgtat---gcttaatgtaataactat-ttgttcttttgta------tttggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGTATTTTGG

upper sequence: GLYMA05G37850.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 10
gttagtttctattggtttcacaattttaac--tggtatctgttgctttgcattggatttgcagcactttccttgttgtgttattgtaaaccattattcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG
| || ||| | ||| || ||| || | | | |||| | || | ||| | | | || || |||| | ||| ||||| ||||| |||||||| | |||||||||||||||||||| || || ||||| ||||||||||| || || |||||||||
------gtttacccttttatctgtttacacgatggcatatctgtcgttgc-taggtatcgcaataactcttgtcttctg-----------cattctgcttg-cagGTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGG

upper sequence: GLYMA05G37850.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G020096_T01 (Zea mays), 3'ss of exon 10
gttagtttctattggtttcacaattttaactggtatctgttgctttgcattggatttgcagcactttccttgttgtgttattgtaaaccattattcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG
|||| | | || | | ||| || ||| | |||| | || ||||| | || | | ||| ||| | ||| ||||| ||| | ||||| || | |||||||||||||||||||| || || ||||| ||||||||||| | || |||||||||
----gtttactcttttgtctctttacatgttggcatatgtgccattgc-taggtattgcaataacttttgtcctctgt-----------attctgcttg-cagGTTAGGTTAAAGAGATACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGG

upper sequence: GLYMA05G37850.1 (Glycine max), 3'ss of exon 11
lower sequence: AT4G23100.3 (Arabidopsis thaliana), 3'ss of exon 11
gttagtttctattggtttcacaattttaactggtatctgttgctttgcattggatttgcagcactttccttgttgtgttattgtaaaccattattcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG
|||| | || | ||| | | | | | | || || |||| | | | ||| ||| || | | |||| | || |||| || ||||||| || |||||||||||||||||||||||||| || ||||| || ||||||| | ||||| || |||
gttaatc---atctgcctcaagagtctttcaatcagcctatgactttcatt----tccctgt-cttatgttgaagtctgacaacgttccataacact----agGTTCGGTTGAAGAGATACTTGGAGATGAGAGGTGCTGATGGAGGTCCCTGGAGGAGGCTGTGTGCCCTGCCAGCTTTCTGG

upper sequence: GLYMA05G37850.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 11
gttagtttctattggtttcacaattttaactggtatctgttgctttgcattggatttgcagcactttccttgttgtgttattgtaaaccattattcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG
||| || | | | || || | || | | || ||| | | | | ||||||| | ||| ||||||||||||||||||| || ||||| ||||| ||||||||||||||||| ||||| || || |||||||| ||||||||||||
--------gtataggcacctgagatcaaattgatgaaattttatatttcttagat--gttgtcacctaagaaatatgttatt---------ttttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG

upper sequence: GLYMA05G37850.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S479_14V6.1 (Physcomitrella patens), 3'ss of exon 10
------------------------------------------------------------------------------------gttagt-ttctattggtttcacaattttaactggtatctgttgctttgcattggatttgcagc------actttccttgt-tgtgttattgtaaaccattattctttt-cagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG
||| || || || || | ||| | | | | | | |||| | | |||| | || || | ||| | | | ||| ||| || ||||| ||||| || | |||||||||||||| || |||||||| || || ||| || |||||||||| || || |||||||||
gtttctagtcattttgtatttcccgtctaatctttgaatacatggataattatagtgagcaatgctcgattctacaagaaatctcttaccattgtactgaattgcccggcttatttattgtgtctagatttgtttcagtcttgctgttggcggacattatgtacgtgtaaattgatggagcatcatttttccgcagGTGAGGCTAAAACGTTATTTGGAGATGAGGGGAGCTGATGGTGGTCCATGGCGACGATTGTGTGCATTGCCTGCATTTTGG

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|12691343|gb|BG157679.1|BG157679
EST:     TACCAACTCTCAATGATTGGGAAAATCACTTGACAACTATATTTCCTGAG                         GTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGG
genomic: TACCAACTCTCAATGATTGGGAAAATCACTTGACAACTATATTTCCTGAGgttagtttct ... ttcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGG
EST: gi|13480024|gb|BG509367.1|BG509367
EST:     TACCAACTCTCAATGATTGGGAAAATCACTTGACAACTATATTTCCTGAG                         GTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGG
genomic: TACCAACTCTCAATGATTGGGAAAATCACTTGACAACTATATTTCCTGAGgttagtttct ... ttcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGG
EST: gi|9900602|gb|BE609570.1|BE609570
EST:     TACCAACTCTCAATGATTGGGAAAATCACTTGACAACTATATTTCCTGAG                         GTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGGCCTTG
genomic: TACCAACTCTCAATGATTGGGAAAATCACTTGACAACTATATTTCCTGAGgttagtttct ... ttcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGA-GGGCCTTG
EST: gi|120494105|gb|EH222272.1|EH222272
EST:     ATGATTGGGAAAATCACTTGACAACTATATTTCCTGAG                         GTCAGNCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGG
genomic: ATGATTGGGAAAATCACTTGACAACTATATTTCCTGAGgttagtttct ... ttcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGG
EST: gi|19453403|gb|BM954813.1|BM954813
EST:     TACCAACTCTCAATGATTGGGAAAATCACTTGACAACTATATTTCCTGAG                         GTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGG
genomic: TACCAACTCTCAATGATTGGGAAAATCACTTGACAACTATATTTCCTGAGgttagtttct ... ttcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGG
EST: gi|120493888|gb|EH222055.1|EH222055
EST:     TACCAACTCTCAATGATTGGGAAAATCACTTGACAACTATATTTCCTGAG                         GTCAGGCTGAAGAGGTATTTGGAGA
genomic: TACCAACTCTCAATGATTGGGAAAATCACTTGACAACTATATTTCCTGAGgttagtttct ... ttcttttcagGTCAGGCTGAAGAGGTATTTGGAGA
EST: gi|207704837|gb|GD684644.1|GD684644
EST:     TACCAACTCTCAATGATTGGGAAAATCACTTGACAACTATATTTCCTGAG                         GTCAGGCTGAAGAGGTATTTGGAGATGCGAGGTGCTGATGGAGGGCCTTGG
genomic: TACCAACTCTCAATGATTGGGAAAATCACTTGACAACTATATTTCCTGAGgttagtttct ... ttcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGG
EST: gi|192299708|gb|FG990032.1|FG990032
EST:     GGGAAAATCACTTGACAACTATATTTCCTGAG                         GTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGG
genomic: GGGAAAATCACTTGACAACTATATTTCCTGAGgttagtttct ... ttcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGG
EST: gi|192303005|gb|FG997021.1|FG997021
EST:     TACCAACTCTCAATGATTGGGAAAATCACTTGACAACTATATTTCCTGGG                         GTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGG
genomic: TACCAACTCTCAATGATTGGGAAAATCACTTGACAACTATATTTCCTGAGgttagtttct ... ttcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attggatttgcagcactttccttgttgtgttattgtaaaccattattcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG
                                       ccattattcttttc  CT-rich tract
 attattctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttctattggtttcacaattttaactggtatctgttgctttgcattggatttgcagcactttccttgttgtgttattgtaaaccattattcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA