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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatttgtgtatacacgaccaagttctttgttttcctgacctagtgcttttccatgtccttcgtgaatcttcattaatgactttggaagcaacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG

Basic information

species Glycine max
transcript GLYMA03G40680.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G40680.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G813143_T02 (Zea mays), 3'ss of exon 4
ttatttgtgtatacacgaccaagttctttgttttcctgacctagtgctt-ttccatgtccttcgtgaatcttcat-taatgactttggaagcaacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG
||    || | ||    ||  | | |||  |||| || | ||   | |  ||  |  ||  |        || || |  |     |  | ||     |||||||| ||||| ||||||||||| ||||| ||||| ||||||||||| || |||| ||||| ||| |  |||||| || | ||  || | ||| |  ||
ttgcaagt-tctaattaactta-tgcttcatttttcttatctttggttcgttgaacatcgatatcatgcatttatctgtttgtcataaatgcttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG

upper sequence: GLYMA03G40680.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G024315_T01 (Zea mays), 3'ss of exon 4
ttatttgtgtatacacgaccaagttctttgttttcctgacctagtgcttttccatgtccttcgtgaatcttcattaat---gactttggaagcaac--acttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG
  |     || |  |    ||  |   |||||      || ||   |    | | | |   ||   ||  ||||  ||   || | |  | ||     ||||||| ||| | || |||||||| ||||||||||| || ||||||||||| ||||||||||| |  |  ||   ||||    |  ||||  |   |  ||||
-gaacaaggtcttaata--catatgtattgttacaaatacgtaa--ccaaacaaagcctaccggatattatcatgtattaagattctttatgctgtggacttcagAGAATTGGGCATTGGAATTGTACCATACAGTCCTCTTGGCCGTGGGTTTTTTGGTGGAAGAGGAGTGAAAGAACAAGTGTCTGCTGAATCTAATCTG

upper sequence: GLYMA03G40680.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0030g01980.t01 (Vitis vinifera), 3'ss of exon 4
-----ttatttgtgtatacacgaccaagttctttgttttcctgacctagtgcttttccatgtccttcgtgaatcttcattaatgactttggaagcaacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG
     ||| |  | ||||  |  |     |||   |||  ||       |  ||||  ||||  ||    |      | |  | | |||| | |      |  || |||||||||||||| ||||| |||||||| || ||||| ||||| |||||||| ||||||| ||| |  |||| |   |||||||||| ||| |||
agaccttaatcct-tatagtctgcagttatctcaatttgtctttttacttaattttatatgtttttaactatgagagaatt-ttattttgtatgtt---ttgtagAGAACTTGGAATTGGGATAGTTCCATACAGTCCTCTTGGACGTGGGTTTTTTGGCGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCTG

upper sequence: GLYMA03G40680.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0030g01990.t01 (Vitis vinifera), 3'ss of exon 4
--------ttatttgtgtatacacgaccaagttctt-tgttttcctgacctagtgcttttccatgtccttcgtgaatcttcattaatgactttg----------gaagcaacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG
        ||   | |   || ||||   | ||  | |  |        |||  | | || |||    | | | |  ||| ||  | ||||| |          ||   |    |  ||||||||||||||||| ||||| |||||||| || || ||||| || |||||||||||||||||||  |  |||| | | ||||||||||||||||||
gtttcgtatttcctatcctta-acgattgattttctatcataaaacattctatagttcttgcattagatccttaatccttaatggaggacttggttacacttgggatatatttttatagGGAACTTGGAATTGGGATAGTTCCATACAGTCCTCTCGGCCGCGGGTTTTTTGGTGGCAAGGCTGCAGGGGAAAATTTGCCTGCAAACAGTTTTCTG

upper sequence: GLYMA03G40680.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0030g02020.t01 (Vitis vinifera), 3'ss of exon 4
-----ttatttgtgtatacacgaccaagttctttgttttcctgacctagtgcttttccatgtccttcgtgaatcttcattaatgactttggaagcaacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG
     ||| |  | ||||  |  |     |||   |||  ||       |  ||||  ||||  ||    |      | |  | | |||| | |      |  || |||||||||||||| ||||| |||||||| || ||||| ||||| |||||||||||||||| ||| |  |||| |   |||||||||| ||| |||
agaccttaatcct-tatagtctgcagttatctcaatttgtctttttacttaattttatatgtttttaactatgagagaatt-ttattttgtatgtt---ttgtagAGAACTTGGAATTGGGATAGTTCCATACAGTCCTCTTGGACGTGGGTTTTTTGGTGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCTG

upper sequence: GLYMA03G40680.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0030g01970.t01 (Vitis vinifera), 3'ss of exon 4
------ttatttgtgta-tacacgaccaagttctttgttttcctgacctagtgcttttccatgtccttcgtgaatcttcattaatgactttggaagcaacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG
       | ||  | |  |  |   || | || | | || |  | ||  | |   |||  ||||  ||    |      | | || | | || | |      |  || |||||||||||||| ||||| |||||||| || ||||| ||||| |||||||||||||||||||| |  |||| | | |||||||||||||| |||
atttatcttttcctctgctgtatttccgatttgtcttttcttttcactcaat---tttatatgtttttaactatgagagacttat-attctgtatgtt---ttgtagAGAACTTGGAATTGGGATAGTTCCATACAGTCCTCTTGGACGTGGGTTTTTTGGTGGCAAGGCTGTTGATGAAAATGTTCCTGCAAACAGTTTCCTG

upper sequence: GLYMA03G40680.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0030g02050.t01 (Vitis vinifera), 3'ss of exon 4
-ttatttgtgtatacacgaccaagttctttgttttcctgacctagtgcttttccatgtccttcgtgaatcttcattaatgactttggaagcaacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG
   |  ||| |  |   | |     | |   ||    |       || ||||       ||   | ||   |     ||| ||||||         |  ||||||||||| ||||| ||||| |||||||| || ||||| ||||| ||||||||||||||||||||    |||| | | |||||||||||||| |||
tccagctgtctgcatctgtctttactataatttcaaattgttctctgtttttattcaatctcttttaactatagaagatgtctttgggtatg-ttttatagGGAACTTGGGATTGGGATAGTTCCATACAGTCCTCTTGGACGTGGGTTTTTTGGTGGCAAGGCTGTTAGTGAAAATGTGCCTGCAAACAGTTTGCTG

upper sequence: GLYMA03G40680.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0030g02060.t01 (Vitis vinifera), 3'ss of exon 4
---------------------ttatttgtgtatacacgaccaagttctttgtt-ttcctgacctagtgcttt--tccatg-tccttcgtgaatc-ttcattaatgactttggaagcaacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG
                         |||  | |  |  |  ||    | | |  ||| ||   |||  | ||  ||| |  |||||  || |    ||  | |  |||| |||   |    |  ||||||||||||||||| ||||| |||||||| || || ||||| || |||||||||||||||||||  |  |||| | | ||||||||||||||||||
gtttcatatttcctatccttaacgattgattttctatcataaaacattctatagttcttgcattagatccttaatccttaatccttaatggaggactcggttac-acttgggatatatttttatagGGAACTTGGAATTGGGATAGTTCCATACAGTCCTCTCGGCCGCGGGTTTTTTGGTGGCAAGGCTGCAGGGGAAAATTTGCCTGCAAACAGTTTTCTG

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|192325845|gb|FK018067.1|FK018067
EST:     TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
genomic: TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAGgtacataaag ... aacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
EST: gi|192298310|gb|FG992100.1|FG992100
EST:     AATTGAGCAAGATATTGTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
genomic: AATTGAGCAAGATATTGTTCCACTTTGCAGgtacataaag ... aacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
EST: gi|192332295|gb|FK025960.1|FK025960
EST:     TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
genomic: TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAGgtacataaag ... aacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
EST: gi|151410675|gb|EV280490.1|EV280490
EST:     TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
genomic: TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAGgtacataaag ... aacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
EST: gi|192314627|gb|FK006385.1|FK006385
EST:     TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAG                         G-AACTTGGA-TTGGA-TAGTACCATACAGCCCC-TTGGC-GTGG
genomic: TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAGgtacataaag ... aacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGG
EST: gi|14125225|gb|BG789655.1|BG789655
EST:     TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTTGATTTTT
genomic: TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAGgtacataaag ... aacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
EST: gi|151411705|gb|EV281516.1|EV281516
EST:     TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
genomic: TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAGgtacataaag ... aacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
EST: gi|209699281|gb|BW670243.1|BW670243
EST:     TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
genomic: TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAGgtacataaag ... aacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
EST: gi|12773659|gb|BG238586.1|BG238586
EST:     TGGTCCCTTTGGACTCGTGAAATTGAGCAAGAT-TTGTTCCACTTTGCAG                         GGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTTGGC-GTGGATTT
genomic: TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAGgtacataaag ... aacacttcagGG-AACTTGGAATTGGAATAGTACCATACAGCCCCCTT-GGCCGTGGATTT
EST: gi|151398884|gb|EV268755.1|EV268755
EST:     TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
genomic: TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAGgtacataaag ... aacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
EST: gi|261497124|gb|GT185192.1|GT185192
EST:     GTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
genomic: GTTCCACTTTGCAGgtacataaag ... aacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
EST: gi|5761333|gb|AI966692.1|AI966692
EST:     TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
genomic: TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAGgtacataaag ... aacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
EST: gi|42722439|gb|CK768339.1|CK768339
EST:     TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTTGGCCGTGGATTTT
genomic: TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAGgtacataaag ... aacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTT-GGCCGTGGATTTT
EST: gi|58017212|gb|CX703954.1|CX703954
EST:     GGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
genomic: GGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAGgtacataaag ... aacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
EST: gi|209701736|gb|BW667401.1|BW667401
EST:     TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
genomic: TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAGgtacataaag ... aacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
EST: gi|213603469|gb|DB966620.1|DB966620
EST:     TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
genomic: TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAGgtacataaag ... aacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
EST: gi|192314626|gb|FK006384.1|FK006384
EST:     TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
genomic: TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAGgtacataaag ... aacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
EST: gi|254315362|gb|GR825171.1|GR825171
EST:     TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
genomic: TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAGgtacataaag ... aacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
EST: gi|7285866|gb|AW598353.1|AW598353
EST:     TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT
genomic: TGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAGgtacataaag ... aacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttttccatgtccttcgtgaatcttcattaatgactttggaagcaacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG
                          cattaat  putative branch site (score: 3)
                        ttcattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatttgtgtatacacgaccaagttctttgttttcctgacctagtgcttttccatgtccttcgtgaatcttcattaatgactttggaagcaacacttcagGGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- -tttgtgt
- - - - - - -cacgacc
- - - - - - - - - - - - - - - - - -ctgacct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gactttg