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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatgcttttgatattctctttagtttcatagtttgtggttgatgctattgattatggaagctttattatggacttagggtatccatcttgaaatatttcactgatttgaatttgaattgtgcctgttgacagCATGTTGAAGATCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTATGGAGTTCCAGGGAAGGATGCTGTGAATTTGGAGG

Basic information

species Zea mays
transcript GRMZM2G156910_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G156910_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g10770.1 (Oryza sativa), 3'ss of exon 6
gtaagatgcttttgatattctctttagtttcatagtttgtggttgatgctattgattatggaagctttattatggacttagggtatccatcttgaaatatttcactgatttgaatttgaattgtgcctgttgacagCATGTTGAAGATCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTATGGAGTTCCAGGGAAGGATGCTGTGAATTTGGAGG
||||||||||| |||||||   | |     |||   ||   |||   | | | | || | ||  |||| || |   |  |   |||||| | ||| || | | ||  | |  |  |||  || || ||  | ||||||||||||||| |||||||| |||||||| |||||||||||||||||||| |||||| ||||||||||||||||||| ||||||||||||||||||||  
gtaagatgcttgtgatattgcttgt-----catgactttctgttctagttgt-gcttcttgattcttttttttc--ccgaaactatccaacctgagatttgttac--actcaa--ttgtgttatgtctactaacagCATGTTGAAGACCATCATTTATACTCACTAAACTACATGCATTGGGGTGCCCCAAAGTTGTGGTATGGAGTTCCAGGAAAGGATGCTGTGAATTTGGAAT

upper sequence: GRMZM2G156910_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA20G36070.1 (Glycine max), 3'ss of exon 4
gtaagatgcttttgatattctctttagtttcatagtttgtggttgatgctattgattatggaagctttattatggacttagggtatcca-tcttga-aatatttcactgatttgaatttgaattgtgcctgttgacagCATGTTGAAGATCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTATGGAGTTCCAGGGAAGGATGCTGTGAATTTGGAGG
                                  || |||| || | |     ||  ||| |  |||  ||   | | |||  | |  | | |||| || |  |   |  |||   | ||  ||     ||    |||||||| |||||||||||||| || ||| |||| ||| |||||||||| |||||||| ||||||||||| || || || || |||||    || ||||| |
----------------------------------gtgtgtgttt-acgtgtgagagaatgaactcttagtt---ggcatagtatctttagttttgataacagctttatattttctttgtggtttaattatggatgcagCATGTGGAAGATCATCATTTATATTCATTGAATTACTTGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG

upper sequence: GRMZM2G156910_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G31510.1 (Glycine max), 3'ss of exon 5
gtaagatgcttttgatattctctttagtttcatagtttgtggttg-atgctattgattatggaagctttattatggacttagggtatcca-tcttga-aatatttcactgatttgaatttgaattgtgcctgttgacagCATGTTGAAGATCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTATGGAGTTCCAGGGAAGGATGCTGTGAATTTGGAGG
                                  || |||| ||  |||  |  ||  ||| |  |||  |||    | |||  | |  | | |||| || |  |   |  |||   | ||  ||     ||    |||||||| |||||||| ||||| || ||| |||| |||||||||||||| |||||||| ||||||||||| || || || || |||||    || ||||| |
----------------------------------gtgtgtgtttacatgtgagaga--atgaatccttagtta---gcatagcatctttagttttgataacagctttatattttctttgtggtttaattatggatgcagCATGTGGAAGATCACCATTTATATTCATTGAATTACATGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG

upper sequence: GRMZM2G156910_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT1G08620.2 (Arabidopsis thaliana), 3'ss of exon 7
gtaagatgcttttgatattctctttagtttcatagtttgtggttgatgctattgattatggaagctttattatggacttagggtatccatcttgaaatatttcactgatttgaatttgaattgtgcctgttgacagCATGTTGAAGATCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTATGGAGTTCCAGGGAAGGATGCTGTGAATTTGGAGG
            ||  ||| || |||  |||| |  || |           ||  || |        |||| |  ||||  |  || | | |||   |  ||   |  ||||  ||||   | | ||||   | |||||||||||||||| || ||||| ||  |||| || ||||| |||||||| || ||  |||||||||| |||   |||||||||||||| ||  | ||||
-----------atgcaattttcatta-cttcacatcttat-----------ttcgtttta-------tattttccacttctgacattccttttgttctgctttttt--tttgtttttg---tttacctga-aatagCATGTTGAAGATCACCACTTGTATTCGTTGAATTATATGCACTGGGGTGCACCGAAATTGTGGTATGGTGTTGGGGGGAAGGATGCTGTTAAACTCGAGG

upper sequence: GRMZM2G156910_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv14s0036g00570.t01 (Vitis vinifera), 3'ss of exon 8
gtaagatgcttttgatattctctttagtttcatagtttgtggttgatgctattgattatggaagctttattatggacttagggtatccatcttgaaatatttcactgatttgaatttgaattgtgcctgttgacagCATGTTGAAGATCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTATGGAGTTCCAGGGAAGGATGCTGTGAATTTGGAGG
                         ||| |  |   |     ||   | | |||||||||     | | || |  | ||   || |   | || |  ||||| | |  ||  |||||      |   ||   ||||||||||||||||||||| || || ||  ||||||||||||| |||||||||||||| || |||||||| || |||||| | |||||  | || |||||||
-------------------------agtat--ttaatgacacttttagatgttgattatgctgattcttttgtttattt---gtttatttgtttatttattt-attttttcaaattta-----tttttgagaacagCATGTTGAAGATCATCACTTATATTCGTTGAACTACATGCACTGGGGTGCTCCAAAAATTTGGTATGGTGTCCCAGGGCAAGATGCCCTTAAATTGGAGG

upper sequence: GRMZM2G156910_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ08267 (Selaginella moellendorffii), 3'ss of exon 2
gtaagatgcttttgatattctctttagtttcatagtttgtggttgatgctattgattatggaagctt-tattatggacttagggtatccatcttgaaatatttcactgatttgaatttgaattgtgcctgttgacagCATGTTGAAGATCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTATGGAGTTCCAGGGAAGGATGCTGTGAATTTGGAGG
                                                        || |  |||||  || | |||   |||      | || || | |    |        |   ||  |  |   | ||  |||||||| || |||||||| || |||||  ||||||||||||| |||||  |||| || || ||||||||||| || ||    |  |||   ||  | ||||
-------------------------------------------------------gtaagttagcttgcatcaaggaacaagg------aactagagaaacg--agaagacaaacgctgtttacttttttttttcagCATGTAGAGGATCATCACTTATACTCGGTGAACTACATGCACTGGGGCTCTCCGAAAATCTGGTATGGAGTCCCCGGCTTTGCGGCTAGCAAGCTAGAGG

upper sequence: GRMZM2G156910_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ29865 (Selaginella moellendorffii), 3'ss of exon 2
gtaagatgcttttgatattctctttagtttcatagtttgtggttgatgctattgattatggaagctt-tattatggacttagggtatccatcttgaaatatttcactgatttgaatttgaattgtgcctgttgacagCATGTTGAAGATCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTATGGAGTTCCAGGGAAGGATGCTGTGAATTTGGAGG
                                                        || |  |||||  || | |||   |||   |  |    ||||          |      |||  | | | | | ||  |||||||| || |||||||| || |||||  ||||||||||||| |||||  |||| || || ||||||||||| || ||    |  |||   ||  | ||||
-------------------------------------------------------gtaagttagcttgcatcaaggaacaaggaactaga----gaaacgagaagacaaacgctgttt--acttttcttttt--cagCATGTAGAGGATCATCACTTATACTCGGTGAACTACATGCACTGGGGCTCTCCGAAAATCTGGTATGGAGTCCCCGGCTTTGCGGCTAGCAAGCTAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtatccatcttgaaatatttcactgatttgaatttgaattgtgcctgttgacagCATGTTGAAGATCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTATGGAGTTCCAGGGAAGGATGCTGTGAATTTGGAGG
                     cactgat  putative branch site (score: 3)
                          atttgaatttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatgcttttgatattctctttagtttcatagtttgtggttgatgctattgattatggaagctttattatggacttagggtatccatcttgaaatatttcactgatttgaatttgaattgtgcctgttgacagCATGTTGAAGATCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTATGGAGTTCCAGGGAAGGATGCTGTGAATTTGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG