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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttgcttgcctgttatatcccagttcttcagatctagcttgggtcgattgctttctttctttatccgttgctgatgctgttgtgtggttgcgatacttcttttatgcagCGTCGACCCTTTCTCTAAGAAGGATTGGTATGACA

Basic information

species Zea mays
transcript GRMZM2G030915_T07
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030915_T07 (Zea mays), 3'ss of exon 1
lower sequence: PP1S80_120V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------gttagtttgcttgcctg-ttatatcccagttcttcagatctagcttgggtcgattgctttctttctttatccgttgctgatgctgttgtgtggttgcgatacttcttttatgcagCGTCGACCCTTTCTCTAAGAAGGATTGGTATGACA-----------------------------------------------------------------
                   |   ||| |  |  ||  ||  || | || || | |  || | ||| ||  |    |     | | | |  ||| |  | ||  |   | ||  |         | | |||||| ||||| |||||||| |||||||||||||||||||                                                                 
gtagcgctctccttctccttctctttacaggaatggctaattcgctgtcctgctgcgctggtttgagtttaggtttcgaggtttgtgtttgtttcc-acgcattgacgcggaggacggtgggatgtaatgcagTGTCGATCCTTTCTCGAAGAAGGATTGGTATGACATCAAGGCCCCCAACACCTTCACGCAGAAGTCGCTGGGGAAGACCCTGGTGACCAGGACCGCGGGT

upper sequence: GRMZM2G030915_T07 (Zea mays), 3'ss of exon 1
lower sequence: PP1S179_15V6.1 (Physcomitrella patens), 3'ss of exon 1
gt-tagtttgcttgcctgttatatcccagttcttcagatctagcttgggtcgatt-gctttctttctt--tatccgttgctgatgctgttgtgtggttgcgatacttc--ttttatgcagCGTCGACCCTTTCTCTAAGAAGGATTGGTATGACA-----------------------------------------------------------------
||  |  || | | |||  |     ||| | | ||   |   ||    || | || |  ||  |||    | | | |||   ||  || | |    | | |||  ||   | || ||||||||||| |||||||| |||||||||||||||||||                                                                 
gtacaccttccctacct--tgccctccattacctccagtgccgcacttgtaggtttgtgttgcttccaaatgttccttgagcat-ttggtctaacatggagatgtttgagtcttgtgcagCGTCGATCCTTTCTCCAAGAAGGATTGGTATGACATCAAGGCTCCTAACACCTTCACGCAGAAGTCGTTGGGGAAGACCCTCGTCACCAGGACGGCGGGT

upper sequence: GRMZM2G030915_T07 (Zea mays), 3'ss of exon 1
lower sequence: EFJ11589 (Selaginella moellendorffii), 3'ss of exon 2
gttagtttgcttgcctgttatatcccagttcttcagatctagcttgggtcgattgct-ttctttctttatccgttgctgatgctgttgtgtggttgcgat-acttcttttatgcagCG--TCGACCCTTTCTCTAAGAAGGATTGGTATGACA
|| |||  | ||| | |     |      |  |    |    |||   ||  |  |    ||||||  |        || | |  |     ||    |   ||||    | | |  |   |||          |  || |     | | |   
gtaagt--gtttggc-gcagcgttttgcctgcttgatttcttctttcctcagTGTCGACCCTTTCTCCAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGA-

upper sequence: GRMZM2G030915_T07 (Zea mays), 3'ss of exon 1
lower sequence: EFJ11647 (Selaginella moellendorffii), 3'ss of exon 2
gttagtttgcttgcctgttatatcccagttcttcagatctagcttgggtcgattgctttctttctttatccgttgctgatgctgttgtgtggttg---cgatacttcttttatgcagCGTCGACCCTTTCTCTAAGAAGGATTGGTATGACA---------------------
           |   |||| |  | |||   ||    || |  ||   | | ||| ||||||   |  |  || |  ||  || |   |  |  |    | |||    |  | ||   ||| ||  |   | |  |   ||| || | |||                      
----------gtaagtgtt-tggcgcagcgttttgcttcgatttta--ttgcttgatttcttctgtcgttagT-GTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGA

upper sequence: GRMZM2G030915_T07 (Zea mays), 3'ss of exon 1
lower sequence: EFJ09804 (Selaginella moellendorffii), 3'ss of exon 2
gttagt-ttgcttgcc-tgttatatcccagttcttcagatctag--cttgggtcgattgctttctttctttatccgttgctgat-gctgttgtgtggttgcgatacttcttttatgcagCGTCGACCCTTTCTCTAAGAAGGATTGGTATGACA---------
|| ||| || |  ||   ||| |    |  || |   | |  |   |||  |||| | |  |     |||| ||       ||| | |    |||    || ||      |||   ||  ||    |   ||   |||| |  |||  | || |         
gtaagtgtttcgcgcagcgttttgcttcgattttattgcttgatttcttctgtcgttagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTT---CAATGTTCGTCAGATCGGGAAGACGC-TTGTGACGAGAACGCAGGGA

upper sequence: GRMZM2G030915_T07 (Zea mays), 3'ss of exon 1
lower sequence: EFJ09763 (Selaginella moellendorffii), 3'ss of exon 2
gttagtttgcttgcctgttatatcccagttcttcagatctagcttgggtcgattgctttctttctttatccgttgctgatgctgttgtgtggttg---cgatacttcttttatgcagCGTCGACCCTTTCTCTAAGAAGGATTGGTATGACA---------------------
                          |||  ||        | || |   | ||| |||||| ||||   |  ||  ||  || |   |  |  |    | |||    |  | ||   ||| ||  |   | |  |   ||| || | |||                      
-----------------------gtaagtgtttggcgcagcgttttgcctgcttgatttctt-ctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctttatccgttgctgatgctgttgtgtggttgcgatacttcttttatgcagCGTCGACCCTTTCTCTAAGAAGGATTGGTATGACA
              tgctgat  putative branch site (score: 3)
                                       tacttctttt  putative PPT
                                          ttcttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttgcttgcctgttatatcccagttcttcagatctagcttgggtcgattgctttctttctttatccgttgctgatgctgttgtgtggttgcgatacttcttttatgcagCGTCGACCCTTTCTCTAAGAAGGATTGGTATGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG