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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttttccaatcccatgcagatttgaatgcattatttatttagcaagtgtgtgttaggagatatcagacaccactctggatggtgagcatgtgcacagtgcacctcattaaaaacttggttgtcctagaatttttatttgcctgacatagcaccatcctgcagATGACCAGGCTTTTGGATATCTTGGAAGATTATCTTATGTATAGGGGATATCAGTATTGTCGAATTGATGGAAATACAGGTGGAGAAGATCGTGATGCAT

Basic information

species Zea mays
transcript GRMZM2G010085_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 10
gtgtgttttccaatcccatgcagatttgaatgcattatttatttagcaagtgtgtgttaggagatatcagacaccactctggatggtgagcatgtgcacagtgcacctcattaaaaacttggttgtcctagaatttttatttgcct--gaca--tagcaccatcctgcagATGACCAGGCTTTTGGATATCTTGGAAGATTATCTTATGTATAGGGGATATCAGTATTGTCGAATTGATGGAAATACAGGTGGAGAAGATCGTGATGCAT
                                                                 ||| ||   | || | | |  | |||||||  ||    ||| |       || ||||||     | |  || | |||| ||  ||||  ||   |||| || ||||||||||||||||||||||| |||||||||||||||||||| || || ||||||||||| || || ||||||||||| ||||||||||||||||||||||
---------------------------------------------------------------tgatctgagttctctattgttcctaagcatgttaacgtcacacat-------aatttggtttcttcaaatcttgtgtttgactttgacatttatgtccattctacagATGACCAGGCTTTTGGATATATTGGAAGATTATCTTATGTACAGAGGCTATCAGTATTGCCGGATAGATGGAAATACTGGTGGAGAAGATCGTGATGCAT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 7
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 10
gtgtgttttccaatcccatgcagatttgaatgcattatttatttagcaagtgtgtgttaggagatatcagacaccactctggatggtgagcatgtgcacagtgcacctcattaaaaacttggttgtcctagaatttttatttgcct--gaca--tagcaccatcctgcagATGACCAGGCTTTTGGATATCTTGGAAGATTATCTTATGTATAGGGGATATCAGTATTGTCGAATTGATGGAAATACAGGTGGAGAAGATCGTGATGCAT
                                                                 ||| ||   | || ||| |  | |||||||  ||    ||| |       || ||||||     | |  |  | |||| ||  ||||  ||   |||| || ||||||||||||||||||||||| |||||||||||||||||||| || || ||||||||||| || || ||||||||||| ||||||||||||||||||||||
---------------------------------------------------------------tgatctgagttctctatggttcctaagcatgttaacgtcacacat-------aatttggtttcttcaaatctcgtgtttgactttgacatttatgtccattctacagATGACCAGGCTTTTGGATATATTGGAAGATTATCTTATGTACAGAGGCTATCAGTATTGCCGGATAGATGGAAATACTGGTGGAGAAGATCGTGATGCAT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 10
gtgtgttttccaatcccatgcagatttgaatgcattatttatttagcaagtgtgtgttaggagatatcagacaccactctggatggtgagcatgtgcacagtgcacctcattaaaaacttggttgtcctagaatttttatttgcctgacatagcaccatcctgcagATGACCAGGCTTTTGGATATCTTGGAAGATTATCTTATGTATAGGGGATATCAGTATTGTCGAATTGATGGAAATACAGGTGGAGAAGATCGTGATGCAT
                                                                   || |      ||| | || |     | |  | | |||   ||     |   ||  |  |   | ||  ||| | |       |  |    |||||||||||||| ||||| ||||| ||||||||||||||||| ||||| | ||| ||||| ||||| ||||||||||| ||||| ||||| |||||||||||||| |
----------------------------------------------------------------gtccacatttttatcttg-tgttttttttatatataatgcttttctgcctatgttttatgttttcataacatttgtgtatacacaactgtgt-atcctgcagATGACTAGGCTCTTGGACATCTTGGAAGATTATCTGATGTACAAGGGGTATCAATATTGCCGAATTGATGGGAATACTGGTGGTGAAGATCGTGATGCTT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 10
gtgtgttttccaatcccatgcagatttgaatgcattatttat-ttagcaagtgtgtgtta--ggagatatcagacaccactctggatggtg-agcatgtgcacagtgcacctcattaaaaacttggttgtcctagaatttttatttgcctgac--atagcaccatcctgcagATGACCAGGCTTTTGGATATCTTGGAAGATTATCTTATGTATAGGGGATATCAGTATTGTCGAATTGATGGAAATACAGGTGGAGAAGATCGTGATGCAT
                                  | | || | | || | |||  | ||   |  |||    |  |   |  |  ||  || | | |||      |    |||||| |    |  |   |   |   || || | | ||| |    | ||      |  |||||||| |||||  | || ||  | ||||||||| | |||| | | |||||||| |||||||| |||||||||||||| ||||| || ||||| ||||| |
---------------------------------gtcagttctgtcagaatgtgattcttgtcgctgatgattgtgaatgccttatattttgcaacctgtttttgtttgctctcattta--tttctgccttttgaattttcttctgtacctaatttgtggcttttctccccagATGACTAGGCTGCTAGACATACTCGAAGATTATTTAATGTTTCGTGGATATCAATATTGTCGCATTGATGGAAATACTGGTGGGGATGATCGAGATGCTT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 10
gtgtgttttccaatcccatgcagatttgaatgcattatttatttagcaagtgtgtgttaggagatatcagacaccactctggatggtgagcatgtgcacagtgcacctcattaaaaacttggttgtcctagaatttttatttgcctgacatagcaccatcctgcagATGACCAGGCTTTTGGATATCTTGGAAGATTATCTTATGTATAGGGGATATCAGTATTGTCGAATTGATGGAAATACAGGTGGAGAAGATCGTGATGCAT
                                              ||  | |||||  | | |          ||||        |||   |||         |  ||| | |   | | || ||  | |  |   |  | || | |  |       | || |||||||| |||||  | || ||  | ||||||||||| |||| | | ||||| || |||||||| |||||||||||||| |||||||| ||||| ||||| |
--------------------------------------------gtcagttctgtgtaggaataagattcttggcactaatagctatgactgtgt--------tatttcaatca--gcctagt-gtatttgt-tccattctcgcttaatctgtggttcttctccagATGACTAGGCTGCTAGACATACTTGAAGATTATCTCATGTTTCGTGGATACCAATATTGTCGCATTGATGGAAATACTGGTGGAGACGATCGAGATGCTT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 10
gtgtgttttccaatcccatgcagatttgaatgcattatttatttagcaagtgtgtgttaggagatatcagacaccactctggatggtgagcatgtgcacagtgcacctcattaaaaacttggttgtcctagaatttttatttgcctgacatagcaccatcctgcagATGACCAGGCTTTTGGATATCTTGGAAGATTATCTTATGTATAGGGGATATCAGTATTGTCGAATTGATGGAAATACAGGTGGAGAAGATCGTGATGCAT
                                              ||  | ||||| || | |          ||||      | | |  |||     | ||       | ||  |      ||| || |  | | |  |||| | |  |       | || |||||||| |||||  | || ||  | ||||||||||| |||| | | ||||| || |||||||| |||||||| ||||| |||||||| ||||| ||||| |
--------------------------------------------gtcagttctgtgtaagaataagattcttggcact------gataactatg-----actgtgttatttcaatcatcctagtgtacttgt-tctattcttgcttaatttgtggttcttctccagATGACTAGGCTGCTAGACATACTTGAAGATTATCTCATGTTTTGTGGATACCAATATTGTCGCATTGATGGCAATACTGGTGGAGATGATCGAGATGCTT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 10
gtgtgttttccaatcccatgcagatttgaatgcattatttatttagcaagtgtgtgttaggagatatcagacaccactctggatggtgagcatgtgcacagtgcacctcattaaaaacttggttgtcctagaatttttatttgcctgac--atagcaccatcctgcagATGACCAGGCTTTTGGATATCTTGGAAGATTATCTTATGTATAGGGGATATCAGTATTGTCGAATTGATGGAAATACAGGTGGAGAAGATCGTGATGCAT
                ||      |  || ||  | |||  | |  |   ||  |||      ||| |  | |    | || |   ||    |||   |       |||||| |    |  |   |   |   || || | ||||| |    | |       |  |||||||| |||||  | || ||  | ||||||||| |  ||| | | |||||||| ||||| || |||||||||||||| ||||| || ||||| ||||| |
--------------gtcagttctgtcagagtgtgtgattcttgtcactgatgattgt----gaataccttatat---tttgcaacctgtttttgtttgc------tctcattta--tttctgccttttgaattttcttctgtgcctaatttgtggtttttctccccagATGACTAGGCTACTAGACATACTCGAAGATTATTTAGTGTTTCGTGGATATCAATATTGCCGCATTGATGGAAATACTGGTGGGGATGATCGAGATGCTT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 10
gtgtgttttccaatcccatgcagatttgaatgcattatttatttagcaagtgtgtgttaggagatatcagacaccactctggatggtgagcatgtgcacagtgcacctcattaaaaacttggttgtcctagaatttttatttgcctgacatagcaccatcctg-cagATGACCAGGCTTTTGGATATCTTGGAAGATTATCTTATGTATAGGGGATATCAGTATTGTCGAATTGATGGAAATACAGGTGGAGAAGATCGTGATGCAT
                                                 || |   |||    | |  |   |    ||       |||         |  |    || | | | | |||  |||        |  |||||     ||  | || |     |  |||||||| ||||||||||||||  | || ||||| || |||||| | || || ||||| || || |||||||||||||| ||||| || || || ||||| |
-------------------------------------------------gtattcattaacgcaaacaaataattgttcctatctttgatt-------ccttttttctgagtgatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 10
gtgtgttttccaatcccatgcagatttgaatgcattatttatttagcaagtgtgtgttaggagatatcagacaccactctggatggtgagcatgtgcacagtgc----acctcattaaaaacttggttgtcctagaatttttatt--tgcctgacatagcacc-atcctgcagATGACCAGGCTTTTGGATATCTTGGAAGATTATCTTATGTATAGGGGATATCAGTATTGTCGAATTGATGGAAATACAGGTGGAGAAGATCGTGATGCAT
             ||   ||| |  | |||| ||  || |  | ||    | ||  ||  ||    ||   ||   |  |   | ||  || ||| ||   | |    ||||||||   |   |  ||    | | |||||| |   ||   ||| |   |   |   | |||||||| ||| |  |||| ||  | ||||||||  | |||| | | ||||| | ||||||||||||||||||||||||||| ||||||||||||||||| |
------------gtcagttgctgtctggaat-caaaatct--tgagt---tatgcattcagatgactcctgcagaccctttttttgtatgcctgtacattattctataacctcattttcattgtatttaatgttgtatttttgtggatgggggaccttctatttaaaattcagATGACAAGGTTGCTGGACATTCTTGAAGATTACTTGATGTTTCGAGGATACCTGTATTGTCGAATTGATGGAAATACAGGGGGAGAAGATCGTGATGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaaacttggttgtcctagaatttttatttgcctgacatagcaccatcctgcagATGACCAGGCTTTTGGATATCTTGGAAGATTATCTTATGTATAGGGGATATCAGTATTGTCGAATTGATGGAAATACAGGTGGAGAAGATCGTGATGCAT
                               gcctgac  putative branch site (score: 3)
                                            ccatcct  putative PPT
                 tagaatttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgttttccaatcccatgcagatttgaatgcattatttatttagcaagtgtgtgttaggagatatcagacaccactctggatggtgagcatgtgcacagtgcacctcattaaaaacttggttgtcctagaatttttatttgcctgacatagcaccatcctgcagATGACCAGGCTTTTGGATATCTTGGAAGATTATCTTATGTATAGGGGATATCAGTATTGTCGAATTGATGGAAATACAGGTGGAGAAGATCGTGATGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA