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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttaattggctcctcctcctgaatatcctagatagataataaaagcttaatagtatgaaacaagtttttcttgataaattctggttttgtgtagtactttcatgcattttacttttaaaaaacttttattcacttcttttccaattttgttttttttttcttctaaaaattcatcttacgtggcagGGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAGCAAAAACCCTTATGGCTATGGAGATCAGGGCTCCACCGATTAACCACTT

Basic information

species Glycine max
transcript GLYMA01G43540.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os08g28730.1 (Oryza sativa), 3'ss of exon 8
gtaagtgttaattggctcctcctcctgaatatcctagatagataataaaagcttaatagtatgaaacaagtttttcttgataaattctggttttgtgtagtactttcatgcattttacttttaaaaaacttttattcacttcttttccaattttgttttttttttcttctaaaaattcatcttacgtggcagGGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAGCAAAAACCCTTATGGCTATGGAGATCAGGGCTCCACCGATTA-ACCACTT
                                                                                                            |   |||||| |  |   |     || |||| |       |  ||| | ||  ||| |  ||||    |  | |       ||| || |||| |||||| ||||| |||||  | ||||||||||| ||||||||||| ||||||||||| || ||    |  | ||||||| |  | | |    
-----------------------------------------------------------------------------------------------------------gtaagttttacatcaacgga-----taatcacatga-----acctttttcttggtttccacctaactggtattgtctttccccagAGCGAAATTTGGCATCGATGAAATGTGTAGGGATCAATGGAACTGGGCTAGCAAGAACCCTTATGGATACGGGTCACTTGACTCCACCAAGCAGAACGGA-

upper sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os09g15420.1 (Oryza sativa), 3'ss of exon 8
gtaagtgttaattggctcctcctcctgaatatcctagatagataataaaagcttaatagtatgaaacaagtttttcttgataaattctggttttgtgtagtactttcatgcattttacttttaaaaaacttttattcacttcttttccaattttgttttttttttcttctaaaaattcatcttacgtggcagGGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAGCAAAAACCCTTATGGCTATGGAGATCAGGGCTCCACCGATTAACCACTT
                                                                                                   |||  || |  || |  || || | || |   | ||| |    || |  | || |  ||||| |      | |   |  ||||| | |  |||||||||||||||||| || || |||||| | || |||||||| ||||| ||||| || ||||  || || |     |  | ||||||| |  |      |
---------------------------------------------------------------------------------------------------gtaagtt-acacagta-acattgagaagatgatcattga----ttgtaaatttctagtttttctcatggtttagtgtcgatcttcctt--cagGGCAAAATATGGCATCGAAGAAATGTGCAGAGACCAATGGAACTGGGCGAGCAAGAATCCTTTCGGGTACGCCTCGCCCGACTCCACCAAGCAGAATGGT

upper sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G469523_T01 (Zea mays), 3'ss of exon 3
gtaagtgttaattggctcctcctcctgaatatcctagatagataataaaagcttaatagtatgaaacaagtttttcttgataaattctggttttgtgtagtactttcatgcattttacttttaaaaaacttttattcacttcttttc-caattttgttttttttttcttctaaaaattcatcttacgtggcagGGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAGCAAAAACCCTTATGGCTATGGAGATCAGGGCTCCACCGATTAACCACTT
                                                                                                            |   |  ||  |  |   |   | | ||  | |           ||| || | | ||   |    || ||| |||| |     || |||||||| || ||||| ||||||||||| || |||||||| ||||| ||||| ||||||||||||||||||   |  | ||| | | |  |      |
-----------------------------------------------------------------------------------------------------------gtaagtcatatatcgaggtataatatgttatcatgacaaaatggctttattgtatattatatgatcaacttcgtcttcctc--tagAGCAAAATACGGTATTGAAGAGATGTGCCGCGACCAATGGAACTGGGCCAGCAAGAACCCTTATGGCTATGGATCACCTGACTCTATCAAGCAGAATGGT

upper sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 8
gtaagtgttaattggctcctcctcctgaatatcctagatagataataaaagcttaatagtatgaaacaagtttttcttgataaattctggttttgtgtagtactttcatgcattttacttttaaaaaacttttattcacttcttttccaattttgttttttttttcttctaaaaattcatcttacgtggcagGGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAGCAAAAACCCTTATGGCTATGGA--GATCAGGGCTCCACCGATTAACCACTT
                                                                                           || |   |  | |   | |   |||  ||| ||||   |  |  | ||      |  || |  || || | |  |||| |    |      | | || |||||| || ||||||||    |||||||| || || |||||||||||||| ||||| ||||| |||||||| | |  |  |    | | |  || |||   || 
-----------------------------------------------------------------------------------------aattagaacataagtgggaaga--tttggtttgaaaatcttggttgtaaccatacatgaaaatgagtcttatgtcacttcaatttgtgtgatgtccctg-cagGGCCAAGTATGGCATCAGCGAGATGTGTCGGGACCAATGGAATTGGGCCAGCAAGAACCCCTATGGCTACGAATCGTCCCCAACACAA--GACTAAAGGCTG

upper sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S101_67V6.3 (Physcomitrella patens), 3'ss of exon 8
gtaagtgttaattggctcctcctcctgaatatcctagatagataataaaagcttaatagtatgaaacaagtttttcttgataaattctggttttgtgtagtactttcatgcattttacttttaaaaaacttttattcacttcttttccaattttgttttttttttcttctaaaaattcatcttacgtggcagGGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAGCAAAAACCCTTATGGCTATGGAGATCAG--GGCTCCACCGATTAACCACTT-
                                                                                                 | || ||| |||   ||||  |  |         | ||   | |  |  | ||| |   || |   ||| | | ||   |  |||  |||  ||| || || | ||||||  | |||||||| |||||||||||||||||||| |  |  ||||| ||||| ||| |||  ||    |  |    | | | ||||   
---------------------------------------------------------------------------------------------gaactcgtgcttacattttttttggtcgtgttttgtaatcatgttcgtggtggcaaatgtaacttctaaattcgttttaac-ctggtctggcgttacagagCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAAAACGAACCCGTATGGATATCGAGGCCAACAAGAACTGGAGGTCA-CCACACA

upper sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S101_67V6.2 (Physcomitrella patens), 3'ss of exon 8
gtaagtgttaattggctcctcctcctgaatatcctagatagataataaaagcttaatagtatgaaacaagtttttcttgataaattctggttttgtgtagtactttcatgcattttacttttaaaaaacttttattcacttcttttccaattttgttttttttttcttctaaaaattcatcttacgtggcagGGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAGCAAAAACCCTTATGGCTATGGAGATCAG--GGCTCCACCGATTAACCACTT
                                                                                                 | || ||| |||   ||||  |  |         | ||   | |  |  | ||| |   || |   ||| | | ||   |  |||  |||  ||| || || | ||||||  | |||||||| |||||||||||||||||||| |  |  ||||| ||||| ||| |||  ||    |  |    | | | ||||  
-------------------------------------------------------------------------------------------aagaactcgtgcttacattttttttggtcgtgttttgtaatcatgttcgtggtggcaaatgtaacttctaaattcgttttaac-ctggtctggcgttacagAGCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAAAACGAACCCGTATGGATATCGAGGCCAACAAGAACTGGAGGTCA-CCACA-

upper sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S221_46V6.1 (Physcomitrella patens), 3'ss of exon 7
gtaagtgttaattggctcctcctcctgaatatcctagatagataataaaagcttaatagtatgaaacaagtttttcttg--ataaattctggttttgtgtagtactttcatgcattttacttttaaaaaacttttattcacttcttttc-caattttgtt----ttttttttcttctaaaaattcatcttacgtg-gcagGGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAGCAAAAACCCTTATGGCTATGGAG---ATCAGGGCTCCACCGATTAACCACTT
      || | |    | ||| ||    || |  |   |             | | ||| ||  |    |||| ||| |  |       || |  || ||| ||    ||||   ||| ||||   |    | ||   || || | |||   |  | | |    |||||  | | |  | || |  | ||  ||  | || || || | ||||||||  || |||||||||||||||||||||||||| |  || || || ||||| ||  |||   |||| |    |   |   |  ||   
------gtaattcaatttctcttc----attttttgcgttatacgctgcttttgactagaattcatttggtttctctagcaactgcacatgatcatg-gtaatatcaccatgtgcttttctttcgtagtcgtgtttggcagttttgttcgtgacatagatgtagtttttaatatacgcacaaattgttttgtgtttgtagAGCTAAGTTTGGCATTGCGGATATGTGCCGTGATCAATGGAATTGGGCAAAAAAGAATCCGTATGGATACCGAGGCCATCAAGAACTCGAGGTCCACGCA---

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|163918103|gb|EH039061.1|EH039061
EST:     GAAATTGTTTATGCATCAACAAAGAAAGCGGAAAGAGAGCTTAAATGGAA                         GGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAG
genomic: GAAATTGTTTATGCATCAACAAAGAAAGCGGAAAGAGAGCTTAAATGGAAgtaagtgtta ... tacgtggcagGGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAG
EST: gi|254337933|gb|GR845396.1|GR845396
EST:     GAAATTGTTTATGCATCAACAAAGAAAGCGGAAAGAGAGCTTAAATGGAA                         GGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAG
genomic: GAAATTGTTTATGCATCAACAAAGAAAGCGGAAAGAGAGCTTAAATGGAAgtaagtgtta ... tacgtggcagGGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAG
EST: gi|254337934|gb|GR845397.1|GR845397
EST:     GAAA-TGTTTATGCATC-ACAAAGAAAGCGGAAAGAGAGCTTAAATGGAA                         GGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAG
genomic: GAAATTGTTTATGCATCAACAAAGAAAGCGGAAAGAGAGCTTAAATGGAAgtaagtgtta ... tacgtggcagGGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAG
EST: gi|16347623|gb|BI973218.1|BI973218
EST:     GAAATTGTTTATGCATCAACAAAGAAAGCGGAAAGAGAGCTTAAATGGAA                         GGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAG
genomic: GAAATTGTTTATGCATCAACAAAGAAAGCGGAAAGAGAGCTTAAATGGAAgtaagtgtta ... tacgtggcagGGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttcttttccaattttgttttttttttcttctaaaaattcatcttacgtggcagGGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAGCAAAAACCCTTATGGCTATGGAGATCAGGGCTCCACCGATTAACCACTT
                                      ttcatctt  CT-rich tract
           aattttgttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgttaattggctcctcctcctgaatatcctagatagataataaaagcttaatagtatgaaacaagtttttcttgataaattctggttttgtgtagtactttcatgcattttacttttaaaaaacttttattcacttcttttccaattttgttttttttttcttctaaaaattcatcttacgtggcagGGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAGCAAAAACCCTTATGGCTATGGAGATCAGGGCTCCACCGATTAACCACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA