Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctgggggtggtgaagtaccctcagtgtcaccactaccacaatcacctgtgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT

Basic information

species Zea mays
transcript GRMZM2G460952_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G460952_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g03460.1 (Oryza sativa), 3'ss of exon 2
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctgggggtggtgaagtaccctcagtgtcaccactaccacaatcacctgtgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
                                                                                                   |   |        |         | || | | | |     |||||    | |||  || | |||||||||||| || ||  |  |  || ||    | ||||  |||||||||||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||||||||||||||| || || || ||||
---------------------------------------------------------------------------------------------------ttttctgcattgctatggtggtgccacttgttcatcatccatcttataaaaaaagaacttgttgttcagcaaaatgatggatactatttatttgacatagGTAAGGGAGATGCCAAATGTTTTAATTCTTCCTCGAAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATCACGATATTGCAGT

upper sequence: GRMZM2G460952_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 3
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctgggggtggtgaagtaccctcagtgtcaccactaccacaatcacctgtgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
                                                                                       || |||||  | |         | |||       |||  ||| |        |  || |  |||   || ||| |  | | || | |      ||    |   || || ||||||  ||||||||| || || || || ||||| || |||||||| ||||||||||| || |||||||||||||| |||||||| ||| |||| || ||  
-------------------------------------------------------------------------------------ctcataatcatatata----tattagattacgtctgtcagtctacaacaatgatagttttaataga---tagattatact-aacatact-----ttgtgtgtgtctgcgt-cagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATATTGCAAA

upper sequence: GRMZM2G460952_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 3
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctgggggtggtgaagtaccctcagtgtcaccactaccacaatcacctgtgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT-
                                                                                |||||  ||||||||  | |        | |  || |    |||  ||| |        |  || |  | |   || ||  || | | || | |      ||  |||   ||  | ||||||  ||||||||| || || || || ||||| |  |||||||| ||||||||||| || |||||||||||||| |||||||| ||| ||||  ||||   
--------------------------------------------------------------------------------ccact--cacaatcatatata----tatatatgtcta----tcagtctacaacaatgatagttttaataca---tagatgatgct-aacatact-----ttgtgcatgtctgcat-caggTGAAGGAGATGCCTAACGTATTGATACTTCCCCAAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATACTACAAAC

upper sequence: GRMZM2G460952_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctgggggtggtgaagtaccctcagtgtcaccactaccacaatcacctgtgacccctcaaaatt-caagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
                                                                               |  |||  |     ||      |  | ||| | || |     |  |  || |  |||||  |||||| || |   ||   | |  | || | |  |  |  ||  |  |  |||    ||||||  ||| ||||||||||| |||||||| || || |||||||| |||||||| ||||| |||||||| ||||| ||||| || ||  |||| || || |
-----------------------------------------------------------------------------gtatgactttcttttccagtgactaaacttcacatttgcgcctgcctattctcttgtttcatcatcttcttctg---ttgtttatcctgcatcca--ttatatcttgttttcattg----cagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT

upper sequence: GRMZM2G460952_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 3
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctgggggtggtgaagtaccctcagtgtcaccactaccacaatcacctgtgacccctcaaaattcaagaactcaac-ctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtga--------ctgatcattgttgtg-tacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
                                                                                                            |||||  || | |   || | ||| |||     | |   | |  ||||     ||||  | ||| | | ||         |  |||||   | || | |||||    || ||||| ||||| || |||||||| || |||||||| || ||||||||||| |||||||| ||||| |||||| | ||   ||| |||||| 
---------------------------------------------------------------------------------------------------------ggaaaaataaaatagccatacacaatattttt----tatgagttaacaattctgcattgtatatcaaggcgatgttaattagccccatcatgactttgcttcagGTAAAAGAAATGCCCAATGTATTGATTCTTCCACGCAGTGCAGATTATAGTGAAGAAGTTTGGATGGAGATAAGGGAGAAAACTATTTGTATATTACAGA

upper sequence: GRMZM2G460952_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S55_132V6.1 (Physcomitrella patens), 3'ss of exon 3
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctgggggtggtgaagtaccctcagtgtcaccactaccacaatcacctgtgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
                                                                 ||||   |  | ||  ||   |  | | || || | |||  |   | | || ||  |  |  || |  |  |     ||| |||  |||||   |||||||           ||||  || ||||  || ||||||| |||| ||||| || || || |||||||| || ||||| || ||||||||||||||||||   || ||| ||   |||||  |  || || |    |
-----------------------------------------------------------------gtacag-cgctatcttcatgtctgctaacagct-tcaccatttctactgcatgatgtttaattacaaatagaatggattcttcattaatta---tttgttc-----------gact--tctttgtcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGTGAAGAAGTGTGGGCTGAGATACGATGCAAAGCCGTCTCTGTGCTGTGCT

upper sequence: GRMZM2G460952_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S35_361V6.1 (Physcomitrella patens), 3'ss of exon 3
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctgggggtggtgaagtaccctcagtgtcaccactaccacaatcacctgtgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
                                                                            ||| | |    ||   |  |   |  |  | ||     ||      |  | |    ||||   || |  |    ||   |    | ||| |  |||   || |    || |  |  | |||||||| ||||||||||||| || || |||||||| || ||||| |||||||| || |||||||||   || ||| |    || || ||  || || |  | |
------------------------------------------------------------------------gtacgtcgctatcttcaactttgcaaatcgcttcccacttccca------ctgcatggtgtttc---atttctaatgaaatcaatgcgtcgttaactaaat--gttatatttcttcatcatatacagGTGAGGGAGATGCCAAACGTCTTGATTCTTCCTCGCAGTGCTGACTACAGCGAGGAAGTGTGGGCCGAGATACGGTCCAAGGCCATCTCTGTGCTGTACT

upper sequence: GRMZM2G460952_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ07708 (Selaginella moellendorffii), 3'ss of exon 3
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctgggggtggtgaagtaccctcagtgtcaccactaccacaatcacctgtgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaatta--cattttgttcagcaaagtggtgact-gatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
                                                                                                                                                  | || |  |     |||| | |  ||   | |  ||| ||    |||| | |||||||  |||||||| |||| || ||||||||||| |||||||| || |||||||| || | |||||  |||||  |    || ||| |  || || |   ||
-------------------------------------------------------------------------------------------------------------------------------------------------gtaagcacctggtttttttatgcgacatgtttggaacttgactcgtgtt-tctacagGTCAGGGAGATGTCAAACGTGTTAATTCTTCCTCGGAGTGCCGATTACAGTGACGATGCGTGGAACGAAATCCGGTTAAAGGCATTTTCTCTGCTGAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
                                 gactgat  putative branch site (score: 3)
      aaattacattttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctgggggtggtgaagtaccctcagtgtcaccactaccacaatcacctgtgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA