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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctgatattctactacatgtaataattccctacttcacattgtgttgtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC

Basic information

species Zea mays
transcript GRMZM2G316967_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctgatattctactacatgtaataattccctacttcacattgtgttgtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC
|||| ||||| ||   | || |     |    |  | | |||   ||     |    |    | |  ||||||       ||    ||||| |||| ||||||||||||||||||||| ||||||||||| ||||||||||| || ||||||||||||||||||||||||||||| ||||||| |||  | ||||| |||
aactaatgttctatttccttgtcacgactattatgttggattcaatggtacatttggtctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 1
aactgatgttgtaccacgttcttttatcccagaa-atggaattgcctgtg-ggctgatattctactacatgtaataattcccta----cttcacattgtgttgtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC
        | |      |    |        |   | | | ||   | |  |||    | || |||     |   | |    ||    ||||  | ||||| | ||||||||| |||| || |||||||| || || ||||||||||| ||||| || || || ||||| |||||||| ||||| ||||  ||||| |||||||| 
-----gcatagcgaagagcctctgggcaatggggtacgaagttttttatatggcatccactcgactgttcatgtcactcttttaaatgcttcttaatgtgt-gcagGCTTGAGAAAGAATCTGGGTTCTTTTTTAACATGAAGTACTTTGAGGAAAAAGTGCAGGCTGGCGAGTGGGAAGAGGTTGAGAAGTACTTATCAGGATTT

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 1
aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctgatattctactacatgtaataattcc-ctacttcacattgtgtt-----gtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC
      | |||       |    |||    | || |     |     |  ||| |   | | | || | | | | || |  | || |  ||| | ||     | ||||| ||| |||| || ||||| |||||||||||||||||||| ||||| || || || ||||| || ||||| || || ||||  |||||  |||| || 
------ttttgatgataataaaattaatttaaaactctttctcttcctttgctaaacatttcccactttttacattttcattgctgcttatttttttctggtgcagGCTCGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G29090.1 (Glycine max), 3'ss of exon 1
aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctgatattctactacatgtaataattcccta----cttcacattgtgttgtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC
   |   ||| |     ||| ||||     |||| |   |||       |||    | || |||     |   | |    ||    ||||  | ||||| | ||||||||| |||| || |||||||| ||||| ||||||||||| ||||| || || || ||||| |||||||| ||||| ||||  ||||| |||||||| 
---tctggttatttagggttttttttataaagaattttcattattatatggcatccactcgactgttcatgtcactcttttaaatgcttcttaatgtgt-gcagGCTTGAGAAAGAATCTGGGTTCTTTTTCAACATGAAGTACTTTGAGGAAAAAGTGCAGGCTGGCGAGTGGGAAGAGGTTGAGAAGTACTTATCAGGATTT

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 2
--aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctgatattctactacatgtaataattccctacttcacattgtgttgtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC
   |    | ||   |  | ||| |||     | |  |   |||   | |       | | || ||  || |  | |||    |  |  | || || || ||||||||| |||| || ||||| |||||||||||||||||||| ||||| || || || ||||| || ||||| || || ||||  |||||  |||| || 
ttgaaaactctttctcttccttcctttgctaaacatttcccatt-tttttcattatctttgctgct-tatttctttattaaaaatgtttctttctggtgcagGCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 1
aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctgatattcta--ctacatgtaataattccctacttcacattgtgttg----tagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC
                 |||  | |||     | ||||  |    ||||   || | |   |  ||  || |    |||  ||  ||   | | ||||     |||||||||| |||||||||| |||||||||||||  ||||| || || ||||| || |  ||||| || |||||||| || ||||  || |||||||| || 
-----------------gttagtctattt---atatggtttgttttgtgttgtgttgtgagaggctgaattttgggattgactgatttgtaatttgttaaatatagGCTTGAGAAAGAGTCAGGATTCTTCTTCAATACCAAGTATTTTGATGAGAAAGTTCTAGCTGGAGAATGGGATGATGTTGAGACGTATTTGTCAGGTTTT

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 1
aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctgatattctactacatgtaataattccctacttcacattgtgttgtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC
   | |  |||| |   ||  ||||          ||   |||  || |      |     | |    ||| |||||    | |     |||   |||||||| |||||||| || || |||||||| || || |||||||| || ||||| |  | |||||| ||||||||||| |||||||  ||  | || || |||
--gtaagtttgtgctttgtcgttttt--------gtgtgcttgtttg-gtttctctgcgtaattttgggta-taatttggaatt---ggttgatgtgtagGCTAGAGCAAGAATCTGGCTTCTTCTTTAACATTAAGTACTTTGAAGAGAAAGCTCTTGCTGGAGAGTGGGATGAAGTGGAGAAGTATCTTTCTGGTTTC

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 1
aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctga---tattctactacatgtaataattcc-----ctacttcacattgtgttgtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC
        || |      ||||| | | ||| |  |  | || | ||   | |     || |  | ||    ||||     |      || ||     ||| ||||||||||||| ||||||||||||| |||||||||||||||||||| |||||||| || || || || || |||||||| || ||||  || || || ||||  
-------tttttttttttttcttcttttcca-atttacactttcttggaagtttggtgtagttaattaatcttaatttgaacggaaattattttttggtgttttgtagGCTTGAGAAAGAGTCAGGGTTTTTCTTCAATATGAAGTACTTTGAGGAGAAAGTACAGGCAGGAGAATGGGATGAAGTTGAGAAGTATTTATCCGGATAT

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 1
aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctgatattctactacatgtaataattc--cctacttcacattgtgttgtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC
  ||| |        |  ||   ||||  |  | ||      ||  |        | ||| ||| | | || | | |   | ||     || | |     ||| | || |||||||| || ||||| |||||||||||||||||||||||  | |||||   ||| || ||||| ||||||||  |||| || || || || 
-cctgcttcaaatgaaacttgagttatttcgaagattttcacgcaagcctctattttttccactgcttttacttactgggcttataatgcactttacc-cagGTTGGAACAAGAGTCCGGATTCTTTTTCAATATGAAGTACTTCGAGGACCAAGTCCAAAGTGGTGAATGGGAGGAGGTGGAACGATATTTATCTGGGTTT

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 1
aactgatgttgtaccacgttctt-ttatcccagaaatggaattgcctgtgggctgatattctactacatgtaataattccctacttcacattgtgttgt-agGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC
       |||     | | |  | | ||     |||||    | |    |      | |||| | |  |||| | | |   |   | | |   | |    ||| | |||||||| ||||| ||||||||||||||||||||||| || ||  | || || | ||| |||||||| ||||||||  |||| || || || |||
--tctgcgttacgtgaagctggtgtcattttcaaaatgtgcatacagacgtttgtttcttctgcaatctgtactgactggttttataataccttctaaccagGTTGGAGCAAGAATCAGGATTCTTCTTCAATATGAAGTACTTTGAAGACCAAGTTCAAGGTGGTGAGTGGGAGGAGGTGGAACGATATTTATCTGGGTTC

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ37833 (Selaginella moellendorffii), 3'ss of exon 1
aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctgatatt-ctactacatgtaataattccctacttcacattgtgttgtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC
                                   ||  |     |||||  || | ||  |  |  ||||||   ||   |  ||         | | ||||| |||||||| || || |||| |||||| ||||||||||| || ||  |||||||   |||||||||||| ||||||||||| |||||||| || |||
----------------------------------gtgagaagatttgtggtttgttcttgttggtggatgtaagtgttgtgtgattt--------tggcagGCTGGAGCAAGAATCTGGCTTCTACTTCAACATGAAGTACTTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ36405 (Selaginella moellendorffii), 3'ss of exon 5
aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctgatatt-ctactacatgtaataattccctacttcacattgtgttgtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC
                                   ||        |||||  |  | ||  |  |  ||||||   ||   |  ||         | | ||||| |||||||| || || ||||||||||| ||||||||| | || ||  |||||||   |||||||||||| ||||||||||| |||||||| || |||
----------------------------------gtgaggagatttgtggtttattcttgttggtggatgtaagtgttgtgtgattt--------tggcagGCTGGAGCAAGAATCTGGCTTCTTCTTCAACATGAAGTACCTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ35798 (Selaginella moellendorffii), 3'ss of exon 1
aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctgatatt-ctactacatgtaataattccctacttcacattgtgttgtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC
                                   ||        |||||  || | ||  |  |  ||||||   ||   |  ||         | | ||||| |||||||| || || ||||||||||| ||||||||| | || ||  |||||||   |||||||||||| ||||||||||| |||||||| || |||
----------------------------------gtgaggagatttgtggtttgttcttgttggtggatgtaagtgttatgtgattt--------tggcagGCTGGAGCAAGAATCTGGCTTCTTCTTCAACATGAAGTACCTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 1
aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctgatatt-ctactacatgtaataattccctacttcacattgtgttgtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC
                                   ||  |     |||||  || | ||  |  |  ||||||   ||      ||         | | ||||| |||||||| || || |||| |||||| ||||||||||| || ||  |||||||   |||||||||||| ||||||||||| |||||||| || |||
----------------------------------gtgagaagatttgtggtttgttcttgttggtggatgtaagtgttgtgcgattt--------tggcagGCTGGAGCAAGAATCTGGCTTCTACTTCAACATGAAGTACTTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgggctgatattctactacatgtaataattccctacttcacattgtgttgtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC
    ggctgat  putative branch site (score: 4)
                  tacatgtaataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctgatattctactacatgtaataattccctacttcacattgtgttgtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- -tgatgtt
- - - - - gtaccac
- - - - - - - - - - - - - - - - - - - - -tgcctgt
- - - - - - - - - - - - - - - - - - - - - - - - -ggctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctacatg