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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgcactttgaatagaagccctatttcaattccatcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG

Basic information

species Zea mays
transcript GRMZM2G091121_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
-----------gtagt-gcactttgaatagaagccctatttcaattccatcccaaaaatctga---ttcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
            | |  |  | ||  || |       | ||    ||  |  ||||| | |||    | |  ||  | |||| ||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||||||||| ||||||||||| |||||||| |||||||| ||||| |
gtttgtttcttatggcagggccttctattggtctatcagttttgctctgtttcaaaattttgaactgtttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG

upper sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 25
-----------gtagt-gcactttgaatagaagccctatttcaattccatcccaaaaatctga---ttcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
            | |  |  | ||  || |       | ||    ||| |  ||||| | |||    | |  ||  |||||| ||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||||||||| ||||||||| | |||||||| |||||||| ||||| |
gtttgtttcttatggcagggccttctattggtctatcagttttgctccgtttcaaaattttgaactatttcattattctttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAATCTTTGAATGAGCTTTATGTTGAAGAGG

upper sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 25
----------------------------------------gtagtgcactttgaatagaagcccta-----tttcaattccatcccaaaaatctgattcttgttgctc------tttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
                                          | |    ||||   |||   | |      ||| ||| | || |   ||   |  |  ||||||||       |||   |||||||| ||  |     | || || || || |||||||||||||| || |||||||| ||||| || ||||| || ||||||||| ||||||  || || |
gtctgcaattttcataccctattgtcaaatgcctacggtttcaatcttatttggtgagataacttgctggctttaaatgctattcagtaataatattgtttgttgcttggattttttattcagGCTGGCCACCTCAGATTAGTTAAGCCGTACATGGTTGCAGTTCAAAGCAACAATGTGTCTGCTGTCAATGAGGCTTTGAATGAAATTTATGCTGAGGAAG

upper sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 25
------------gtagtgcactttgaatagaagccctatttcaattccatcccaaaaatctgattcttg-ttgctctttgg------acagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
            || ||  |  || |||   |      ||    || ||| ||| || ||| ||       | | ||||        | ||||||||||  | | |||||||||||||||||||||||||||||| || ||||| || ||||| || |||||||| ||||||||  | ||||| || || |
gtaggatcattagtggtaaaaatttaattagatattagtt---gttgcatgccataactctaatgggaaacttcactttaatatgctatagGCTGGTCACCTCCGTCTTGTGAAACCATATATGGTTGCAGTTCAAAGCAACAACGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTTGAGGAGG

upper sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
--------------------------gtagtgcactttgaatagaagccctatttcaattccatcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
                           |  |    |||   |   | ||   |||| ||| ||  | |  ||| |  | | |||      ||  | ||||||||||  | | |||||| || ||||| |||||||||||||||||||||||||| ||||| || ||||||||| | |||||| | ||||| || || |
gtagcattaatactgtcaacaatttcatcttaatttttactttataacctgttttccatttcactctatgaatattttccctgtgatgtatt--atagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG

upper sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
gtagtgc-actttgaatagaagccctatt-----tcaattc---catcccaaaaatctgat------tcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
||||    | | |    | ||     |||     ||| ||    ||| ||| ||  || ||      | |  ||| | |    | ||||||||||  | | |||||||||||| |||||| |||||||||| || |||||||| ||||| || |||||||| ||||||||  | |||||||| || |
gtaggatgaatattggcaaaaatttcattagatatcagttgttgcatgccataacactaatgggaaatttcattgatatgct-atagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG

upper sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 23
--------------------------------------gtagtgcactttgaatagaagcc----ctatttcaa----ttccatcccaaaa----atctgattcttgttgctctttggac---agGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
                                       || |   ||||   |  |        || ||| ||    ||  || | | |     || || | |||| |  | | |||     ||||||| ||  | |   | || || || ||  ||||||||||||| || || ||||| ||||| || |||||||| ||||||||| ||||||| || || |
gtctgtaggtctcattctattttctaatgtgttaagttttaatcttcttttggtgaagttaataactgtttgaaaatattttatgcaatattcttatttgttgcttgattttttctggtttttagGCTGGCCACATCCGATTGGTTAAGCCGTACTTGGTTGCAGTTCAAAGCAATAATGTGTCTGCTGTTAATGAAGCTTTGAATGAAATTTATGTTGAGGAGG

upper sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 24
--------------------------gtagtgcactttgaatagaagccctatttcaattccatcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
                           |  |    |||   |   | ||   |||| ||| || |  |  ||| |  | | |||      ||  | ||||||||||  | | |||||| || || || ||||||||||||||||||||||| || ||||| || ||||||||| |||||||| | ||||| || || |
gtagcattaatactgtcaacaatttcattttagtttttactttataacctgttttccatttca-ctgatgaatattttccctgtgatgtatt--atagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG

upper sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 25
---------------------------------------gtagtgcactttgaatagaagcccta-----tttcaattccatcccaaaaatctgattcttgttgctc----tttgga----cagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
                                         | |    |||| | |||     |      ||  ||| | || |   ||   |  |  ||||||||     |||  |    |||||||| ||  |     | || || || || |||||||||||||| || |||||||| || || || |||||||| ||||||||| ||||||| || || |
gtctgcaatttcataccctattgccaaatggctacagtttcaatcttatttggagagataatttgctggtttcaaatgctattctgtaatagtattgtttgttgcttggattttttattttcagGCTGGCCACCTTAGATTAGTTAAGCCGTACATGGTTGCAGTTCAAAGCAACAATGTGTCCGCTGTCAATGAAGCTTTGAATGAAATTTATGTTGAGGAAG

upper sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
-----------------gtagtgcactttgaatagaagccctatttcaattccatcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
                 |   |    |||   || ||   | | |    | |  | |  || |  || ||  |  || |||     ||||||||||| |||| |||| | || ||||| ||| ||||||||||||| |||||||||||||| || ||||| ||  |||||||  | || || ||||| |
gttagaagctgactgatgactttgtttttttctataaaaacaactgagctacattacttaacaattggtttcttctgatct-----cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG

upper sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
------------------gtagtgcactttgaatagaagccctatt-tcaattccatcccaa---aaatctgattcttgttgctc--tttgga---cagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
                   |     | |||   |  ||  | |||   || |  | |  |||   | |||||||  || || ||   ||  ||   ||||||||||| ||||  ||| | || ||||||||||||||||||||||| || ||||| ||||| || ||||||||  |||||||  | ||||  ||||| |
gttagaggctgaccattgatttaatattttctgttaaaaacttatcaccagtggcttaacaatctatatctgatgattatttcttgtttctgatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG

upper sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 25
------------------------------------------------------gtagtgcactttgaatagaagccctatttcaattccatcccaaaaatctgattcttgttg-ctctttgga---cagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
                                                      || |       ||| || |||    |      ||   ||      |||| || ||| |   ||||||||    |||||||||||  | ||||||||||| || ||||||||||| ||||||||||  |||||  |||| || |||||||| || ||||   || |||| || || |
gtctgcatgtttgcttactctttatgtgatggatattgctgtgtgcttcttttagtgggaacaaatgattaaaagtttaaaaatggttttgtcaatggtatcttatgcttatgatctctttgggtttcagGCTGGTCACCTTCATCTTGTGAAGCCCTATATGGTTGCTGTTCAGAGTACTAATGTGGCTGCGGTAAATGAAGCATTAAATGGTATTCATGTAGAGGAGG

upper sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
--------------------------------------------gtagtgcact--ttgaatagaagccctatttcaattccatcccaaaaatctgattct-tgttgctctttgga---cagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
                                            | |||    |  |||  |    | |   | |  |         |    | || || |  |||  |  |||||   ||||| |||||  | ||||||||||| |||||||||||||||||||||||||||||||| ||||| |||||||| || |||||||   ||||||| || || |
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagccctatttcaattccatcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
                            atctgat  putative branch site (score: 4)
                                  ttcttgttgctcttt  CT-rich tract
       tatttcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgcactttgaatagaagccctatttcaattccatcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG