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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatgggtcctatgctgtttttattgattttactgtattttgttaaattacatttatttgtcttggttatcgctaatcatttcttgtaccctttgatgtatagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC

Basic information

species Zea mays
transcript GRMZM2G057576_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 12
gtaagatgggtcctatgctgtt--tttattgattttactgtattttgttaaattacat-----ttatttgtcttggttat-cgctaatcatttcttgtaccctttgatgtatagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
|||| ||||||  || | ||||  || ||||    ||  | ||||||||| | |   |     ||   ||||| | || | |  ||||   | | || || ||||| ||||  ||||||||||||||||||||| |||||||||||||| ||||| ||||||||||||||||||||||| |||||||||||||| ||||| |||||||| || |
gtaaaatgggtgttaagttgtttgttgattgcacatatcg-attttgttacactgtgtcctgtttgactgtctggattgttcattaattgatacctgcactctttggtgta--gACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 12
gtaagatgggtcctatgctgtt--tttattgattttactgtattttgttaaattacat-----ttatttgtcttggttat-cgctaatcatttcttgtaccctttgatgtatagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
|||| ||||||| || | ||||  || ||||    ||  | ||||||||| | |   |     ||   ||||| | || | |  ||||   | | || || ||||| ||||  ||||||||||||||||||||| |||||||||||||| ||||| ||||||||||||||||||||||| |||||||||||||| ||||| |||||||| || |
gtaaaatgggtcttaagttgtttgttgattgcacatatcg-attttgttacactgtgtcctgtttgactgtctggattgttcattaattgatacctgcactctttggtgta--gACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 12
---------------------------------------------------gtaagatgggtcctatgctgtt-tttat-tgattttactgtatt--ttgttaaattacatttatttgtcttggt-tatcgctaatcatttcttgtaccctttgatgt-atagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
                                                    |  | | | | || |    || ||||  | ||  ||   || |  ||||| ||||   ||  | ||   |||| |||   |  | ||||    ||   | |    |  |||||||||||||||||||||||  | |||||||||||||| ||||| || || || ||||||||||||||||||||||| || |||||||||||||| || |
gttgggttgcatttgaaattttgaaaaactctaaactgatctgtttattttttgcgtttgtttctttctaattgtttacctaatagtataatactgcttgttgaatttgcttattatgaaatggtatatttgtgttaattttgattaatatgttccattgtagACTGTGGACAATGATCTTGCTTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 12
gtaagatgggtcctatg---ctgtttttattgattttactgtat-------tttgttaaattacatttatttgtcttggt-tatcgctaatcatttcttgtaccctttgatgt-atagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
||  | | |    |||     || |||| || |  | |  ||||        ||||| ||||   ||  | ||   |||| |||   |  | |||| |  ||   | |    |  ||||||||||| |||||||||||  | |||||||||||||| ||||| || || || ||||||||||||||||||||||| || |||||||||||||| || |
gttgggttgcatttataattttgcttttgtttacctaatagtatactactgcttgttgaatttgcttattatgaaatggtatatttgtgttaatttttattaatatgttccattgtagACTGTGGATAATGATCTTGCCTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 12
----------------------------------------gtaagatg-ggtcctatgctgt-ttttattgatt--ttactgtattttgttaaattacatttatttgtcttggttatcgctaatcatttcttgtaccctttgatgtat----------agACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
                                        || |  |       | | || | | ||  | |||   | |   |  | |   | | |   | || |  | || |||| |  ||   ||   |  ||  ||  | | ||          ||||||||||||||||||||||  | |||||||| ||||| ||||| || || || |||||||||||||| |||||||| |||||||||||||||||||| |
gttgggttgcattaaaatttgaaaaattcaatattattctgttatttataactttgtactctatctttctaattgtctgccaaaaatagggtactgattctcatctaacctgtttattgtgaaatgttgtattaacttttacaagcatgctcccttgtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCGTTTGCTGAGAGGAGGGAGTTTGACAAAATTC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 12
------------------------------------------------gtaagatgggtcctatgctgttttt---attgattttactgtattttgttaaatt-acatttatttgtcttggttatcgctaatcatt----tcttgtaccctttg-----atg------tatagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
                                                 |||  | | |  ||  || | |||   ||||  |       || | |    | | |   | || |  | || |||| |  ||   ||    |||  ||   |||      |||      | |||||||||||||||||||||||  | |||||||| ||||| ||||| || || || |||||||||||||| |||||||| |||||||||||||||||||| |
gttgggttgcattaaaattttgaaaaattcaatattattttgttatttataactttgcttgtactctatctttctaattgtctcccaaaaatataggggtactgattctcatctagcctgtttattgtgaaatgttgtattctattaatttttacaagcatgctcccttgtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCATTTGCTGAGAGGAGGGAGTTTGACAAAATTC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 12
gtaagatgggtcctatgctgtttttattgattttactgtattttgttaaattacatt-tatttgtcttggttatcgctaatcatttcttgtaccctttgatgtatagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
 ||       |  |    |  ||  |  || || | ||| ||||   |  || | || | ||| | ||| | |||  ||       | || |   | | | | |  ||| ||||| ||||| || ||| |||||||||  ||||| ||||| || || || ||||||||||| || |||||||| |||||||| |||||||| || |
ttactgccattttttatttccttcaagggaattcaatgtctttt--cagtttgctttatttttattttgctgatctttatgagagacatgca---tataacgca--gACAGTGGATAATGACCTCGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 12
gtaagatgggtcctatgctgtttttattgattttactgtattttgttaaattacatttatttgtcttggttatcgctaatcatttcttgtaccctttgatgtatagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
 | |  |   |   | |    |  |  |   ||  |||  || ||||   | ||| || | |  |||  || || |||||  || |  |       |    |  |||| ||||| ||||| |||||| ||||||| || || || || || || || || ||||||||||| |||||||| || |||||||| ||||| || || |
-tcaattccttttaaaggaactcattctctgttccctgatttgtgtt---tcacacttctat-cctttattttc-ctaatttttacgaggcttgcatataatgcagACAGTGGATAATGACCTTGCATTGAAAATTTATATTAAAGCTAGAGCCACACCAAAAGTTGTTGCAGCTTTTGCGGAGAGGAGGGAATTTGATAAGATCC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 12
------------------------------------------------------------------------------------gtaagatgggtcctatgctgtttttattgattttactgtat-tttgttaaattacattt---atttgtcttggttatcgctaatcatttcttgtaccctttgat--gtatagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
                                                                                    | |||     ||| |     |||| || ||  | | | | | ||   | | ||   |||   | || | |   ||||         |||  ||   | |   |    | ||||| ||||| ||||| |||||| ||||||| || ||||| || || || || || ||||||||||| |||||||| || |||||||| ||||| || || |
gtcctgacagaaatttaaattgttttatctttttcatatgaacttatttattagttttatttcatggacagtttgggtgtttggggaaggaaaatccaaattccttttaatggaactcattctctgttccctgatttgtgttttgcacttctatcctttattttcccaatttttatgaggcttgcaaataatgtagACAGTGGATAATGACCTTGCATTGAAAATTTATATCAAAGCTAGAGCCACACCGAAAGTTGTTGCAGCTTTTGCAGAGAGGAGGGAATTTGATAAGATCC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaagatgggtcctatgctgtttttattgattttactgtattttgttaaattacatttatttgtcttggttatcgctaatcatttcttgtaccctttgatgtatagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
                     |  | || |  | ||  | ||   ||||| |   |    | | |||  |||         |    |  ||   | ||||  |  ||||||||| ||||| ||||| || |||||||||||||| || || || || || ||||| ||||| |||||||| ||  | |||||||||||||||||| 
--------------------gtaatcttaaaatgaccattttcatttaaagtgtctcctatgggcttctttagtatgctgtaacggtaatattttctgattca--gACTGTGGATAATGACCTTGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATAT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaagatgggtcctatgctgtttttattgattttactgtattttgttaaattacatttatttgtcttggttatcgctaatcatttcttgtaccctttgatgtatagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
                     |  | ||||  |    |  |||  | ||| |   |  || |||||    ||| |    |  |  |    | |||||    |  |||||||||| |||||||| || ||||||||||||||||| ||  |||| || || |||||||| || |||||||| ||||| |||||||||||||||||||
--------------------gtaatcttgaaatggacgattttattcaaaatgtgtg-atatgtctc--ctatggtgtgttgtgacgataaacctttctgttccagACTGTGGATAATGATCTCGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATAC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 12
gtaagatgggtcctatgctgtttttattgattttactgtattttgttaaattacatttatttgtcttggttatcgctaatcatttcttgtaccctttgatgt-atagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
   |  |||     |   || | | | |  ||||    |  | ||||  |||   | | |||  |||  || | |    ||   | |||||     | |  |  ||||| ||||| ||||| ||||||||||||||||| ||||| || ||||| || || ||||||||||| || |||||||| ||||||||||| || ||||| |
---acttggaaaggagtatggtct-aatagttttttcatgctctgtttgatt---tgtgtttcccttccttttggtctttctgatgttgtaattgctaacattgtagACGGTGGATAATGACCTTGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 12
--------------------------------------gtaagatgggtcct------atgctgttttta-ttgattttactgtattt----tgttaaattacat--ttatttgtcttggttatcgcta-atcatttcttgtaccctttgatgtatagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
                                       |||||    || |      |||||  ||| | || |||||| | | |||    || ||| ||| ||  || ||| | ||   |||   |    ||||          |||  | | ||||||||||| | ||| |||||||| |||||||| || || || || ||||| || ||||||||||| || ||||||||  |  |||||||||||||||| |
gtttgaaatgcaattggagatgattattttttgtccacttaagacaattcttgttgggatgctaatttgagtttattttattatttttatcctgctaatttaaatgatttttttttttaaatataattttgacattgaaaaccatgttttttttgtagACTGTGGATACTGACCTTGCACTCAAAATATATATTAAAGCGAGAGCAACTCCGAAAGTTGTTGCAGCCTTTGCTGAGCGTCGGGAGTTTGACAAAATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatttatttgtcttggttatcgctaatcatttcttgtaccctttgatgtatagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
                               tttcttgtacccttt  CT-rich tract
                         taatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatgggtcctatgctgtttttattgattttactgtattttgttaaattacatttatttgtcttggttatcgctaatcatttcttgtaccctttgatgtatagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG