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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatcaataccttcactggtccctaaatattctaatgagatttgccgtggtcaaccatgacaaggtttttaatcattaagtgtgacttgaaacttggcagGTGGCAATGACGCATCCAATGGCAGTCACCAACTGCAACATTGATATGGAAAGTTTAATCTCTGACCAGAACAGAAGCATTGCTACCCTTGCTATTACTA

Basic information

species Glycine max
transcript GLYMA06G01520.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 3'ss of exon 8
aaatcaataccttcactggtcc--ctaaatattctaatgagatttgccgtggtcaaccatgacaaggtttttaatcattaagtgtg-acttgaaacttg----gcagGTGGCAATGACGCATCCAATGGCAGTCACCAACTGCAACATTGATATGGAAAGTTTAATCTCTGACCAGAACAGAAGCATTGCTACCCTTGCTATTACTA
       | |||    || |     ||||   | |  | | | |     || |   |  ||        || | |      ||||  | |||| | |       ||||| |||   || |||||  |||| |||||||| || ||||| |||||||| |||||||| ||||| |||||||| ||||||||||||||||| ||||| |
------gttcctcttttgattatattaaactgtatgcttatactatgtttgataggct-tgttggttccttcacttgacttgtgttcatttgatattgattgtacagGTTGCATCAACTCATCCTTTGGCTGTCACCAATTGTAACATAGATATGGAGAGTTTAATATCTGATCAGAACAGGAGCATTGCTACCCTTGCAATTACAA

upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 8
----aaatcaata--ccttcactggtcccta--aatattctaatgagatttgccgtggtcaaccatgacaaggtttttaatcattaagtgtgacttgaaacttggcagGTGGCAATGACGCATCCAATGGCAGTCACCAACTGCAACATTGATATGGAAAGTTTAATCTCTGACCAGAACAGAAGCATTGCTACCCTTGCTATTACTA
      ||  |||   |  ||| | |  ||   | ||||||  | ||| | |  ||  |  |  || | |   ||  | |    |  |||||| |   || |   ||||| |||   || |||||  |||| ||||| || || ||||| || ||||| || ||||||||||| |||||||| |||||||| |||||||| ||||| |
ttccttattgataatacgacacagatttcttgtagtattcttgtcagaatcgttgttattca--attatat--ttactgactgctc-gtgtgaat---aattgtacagGTTGCATCAACTCATCCTTTGGCTGTCACAAATTGTAACATAGACATGGAGAGCTTAATCTCTGATCAGAACAGGAGCATTGCAACCCTTGCGATTACAA

upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 8
---------aaatcaataccttcactggtccctaaatattctaatgagatttgccgtggtcaaccatgacaaggtttttaatcattaagtgtgacttgaaacttggcagGTGGCAATGACGCATCCAATGGCAGTCACCAACTGCAACATTGATATGGAAAGTTTAATCTCTGACCAGAACAGAAGCATTGCTACCCTTGCTATTACTA
          | |  ||  |   | |  || |  | | ||||  | ||| |    ||  |  |  || | |   ||  | |   || | ||||| |   || |   ||||| |||   || |||||  |||| ||||| || || ||||| || ||||| || ||||||||||| |||||||| ||| |||| |||||||| ||||| |
tttcttattgattgtatggcacaaatt-tctcggagtgttcttgtcagaatcattgttattca--attatat--ttactgactgttca-tgtgaat---aattgtacagGTTGCATCAACTCATCCTTTGGCTGTCACAAATTGTAACATAGACATGGAGAGCTTAATCTCTGATCAGAACAGGAGCGTTGCAACCCTTGCAATTACAA

upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 7
------------------------------aaatcaataccttcactggtccctaaatattctaatgagatttgccgtggtc--------aaccatgacaaggtttttaatcat----taagtgtgacttgaaacttggcagGTGGCAATGACGCATCCAATGGCAGTCACCAACTGCAACATTGATATGGAAAGTTTAATCTCTGACCAGAACAGAAGCATTGCTACCCTTGCTATTACTA
                              | ||  | |||   | || |   | | ||||||    |||||   | |   |         |  ||||  || | ||| |   |    |||     | ||  |||    ||||| |||||||| ||||| ||||| |||||||||||||||||||||||||| |||||||||||||| || || |||||||||||||| || || || || |
gtttgcaatgctttcaactgttctctttgtacattgacaccgaaa-tgatgttttactattctgggtagattcatcattacctttatcatgaggatgaggagatatttcactgtatactaaacacaagtttgaacc--acagGTTGCAATGACTCATCCTATGGCTGTCACCAACTGCAACATTGATATGGAGAGTTTAATCTCTGATCAAAATAGAAGCATTGCTACACTCGCAATAACCA

upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 8
aaatcaataccttcactggtccctaaatattctaatgagatttgccgtggtcaaccatgacaaggttttta----atcattaagtgtgacttgaaa--cttggcagGTGGCAATGACGCATCCAATGGCAGTCACCAACTGCAACATTGATATGGAAAGTTTAATCTCTGACCAGAACAGAAGCATTGCTACCCTTGCTATTACTA
      || |      ||  |  |||  ||| |  | |    ||   | | | |  || ||||  ||||||    |  | |||   | | ||  ||  ||| ||||||||||||||| ||||||||||| || || ||||||||||| |||||||||||  |||| ||||||||||||||||||||||| || || || || || |
---gtgatgctcattttga-ctataatcattttgctaa--cctgattttgaccatgataacaaaatttttataataataataatcttaaatttgaattctttgcagGTGGCAATGACACATCCAATGGCTGTAACTAACTGCAACATAGATATGGAAAGCCTAATTTCTGACCAGAACAGAAGCATTGCAACACTGGCAATCACCA

upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S15_298V6.2 (Physcomitrella patens), 3'ss of exon 7
-aaatcaataccttcactggtccctaaatattctaatgagatttgccgtggtcaaccatgacaaggtttttaatca-ttaagtgtgacttgaaa----cttggcagGTGGCAATGACGCATCCAATGGCAGTCACCAACTGCAACATTGATATGGAAAGTTTAATCTCTGACCAGAACAGAAGCATTGCTACCCTTGCTATTACTA
   | || |    |||||| || | | || |       | || || |      |   ||  ||    ||  | | |  |    ||  | ||       |||  ||||| |||  ||| || ||| |||||||  |||||||||||||||| ||||||||| | || |||||||| ||| | ||||||||||| ||||| |||||||
aggagcattgaagtcactgttctccacatctc------atatctgtcagaactatttattccatttcttccactaagcttgaggtttcctggggttgtctttccagGTTGCACAGACCCAGCCATTGGCAGTTGCCAACTGCAACATTGACATGGAAAGTCTCATATCTGACCAAAACCGCAGCATTGCTACTCTTGCCATTACTA

upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S41_154V6.1 (Physcomitrella patens), 3'ss of exon 8
aaatcaataccttcactggtccctaaatattctaatgagatt-tgccgtggtcaaccatgacaaggtttttaatcattaagtgtgacttgaaacttg-gcagGTGGCAATGACGCATCCAATGGCAGTCACCAACTGCAACATTGATATGGAAAGTTTAATCTCTGACCAGAACAGAAGCATTGCTACCCTTGCTATTACTA
  ||   | |       |     ||||     || |    || |    |      | ||  |  |     ||| ||||  || |     |    ||  |||||| |||  ||| |||||| | |||||||||| ||||||||| || ||||||||| | || |||||||| ||| | ||||||||||| ||||| || ||||
gtattgttgcggatgaagactagtaaaggcattattttacttatattatacctgtcaatcgcttg--cactaagcattttgtttcctcgggttgttatgcagGTTGCACAGACCCATCCATTAGCAGTCACCAGCTGCAACATCGACATGGAAAGTCTCATTTCTGACCAAAACCGCAGCATTGCTACTCTTGCAATCACTA

upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S276_96V6.1 (Physcomitrella patens), 3'ss of exon 8
--aaatcaataccttcactggtccctaaatattctaatgagatttg---ccgtggtcaaccatgacaaggtttttaatcattaagtgtgacttgaaacttggcagGTGGCAATGACGCATCCAATGGCAGTCACCAACTGCAACATTGATATGGAAAGTTTAATCTCTGACCAGAACAGAAGCATTGCTACCCTTGCTATTACTA
   |    | |  |   |     | |||   ||  ||  |    |      |||  ||    |  ||    |  |  || ||   || |  |     ||| | |||| |||  ||| |||||| |||||||  ||||||||||  |||| ||||||||| | || |||||||| ||| | ||||||||||| || || || ||||
ctgaggttacagttctgc-acctcttaatcgttacaaccatccatcaatttgtgtccatttctttcactaatcatgttc-ttttttggggtt---gtctttgtagGTTGCACAGACCCATCCACTGGCAGTTGCCAACTGCAATGTTGACATGGAAAGTCTCATTTCTGACCAAAACCGCAGCATTGCTACTCTAGCCATCACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtggtcaaccatgacaaggtttttaatcattaagtgtgacttgaaacttggcagGTGGCAATGACGCATCCAATGGCAGTCACCAACTGCAACATTGATATGGAAAGTTTAATCTCTGACCAGAACAGAAGCATTGCTACCCTTGCTATTACTA
                     ttttaat  putative branch site (score: 3)
                    tttttaatcattaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatcaataccttcactggtccctaaatattctaatgagatttgccgtggtcaaccatgacaaggtttttaatcattaagtgtgacttgaaacttggcagGTGGCAATGACGCATCCAATGGCAGTCACCAACTGCAACATTGATATGGAAAGTTTAATCTCTGACCAGAACAGAAGCATTGCTACCCTTGCTATTACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - -ccttcac
- - - - - - - - - - ccctaaa
- - - - - - - - - - - - - - - - - - - - - tgccgtg
- - - - - - - - - - - - - - - - - - - - - - - - - -caaccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtgac