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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcttctcctgctccgtccatccgactgcggtgattagaatttgatccatgggtttgatttagcccctgctttcgcacctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAAGTCCGCG

Basic information

species Zea mays
transcript AC230013.2_FGT007
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC230013.2_FGT007 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g47660.1 (Oryza sativa), 3'ss of exon 1
gtgagtcttctcctgctccgtccatccg--actgcggtgattagaatttgatccatgggtttgatttagcccctgctttcgcacctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAAGTCCGCG
                      || |||   || |||||  |         ||| || |||||||| | |       | ||     |||||||||||||||||||||||||||||||||||||||||||| |||||||| |||||||||||||||||||| |||||||||||||||||||| || |||||||
-----------------gtaagcagccgttgcttcggtggatgtggccgcctccgtgcgtttgattgatctgtcctctccgtgtgcgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACCCCCGGCGATGAGCACCCCAAGATCTACCGGATGAAGCTCTGGGCCACCAATGAGGTCCGCG

upper sequence: AC230013.2_FGT007 (Zea mays), 3'ss of exon 1
lower sequence: PP1S5_178V6.1 (Physcomitrella patens), 3'ss of exon 1
------------gtgagtcttctcctgctccgtccatccgactgcggtgattagaatttgatccatgggtttgatttagcccctgctttcgcacctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAAGTCCGCG
               |   |  || ||     |  |     ||    |  |      ||  ||  ||| | |||||| |  | |  || |    |    ||||| || || ||||||||||||||||| || || || ||  |   | | |||  ||| ||    |||||||||||||| ||||| ||||| ||||||||||
atttggtgtcattgaaaaatggtcgtgagtttttgaatgtcctttttttttccccccttcttctttggttctgatttggttcattattccttgtca--acagTTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAGGCCCCTAAAGCTTACCGCATGAAGCTTTGGGCGACCAATGAAGTCCGCG

upper sequence: AC230013.2_FGT007 (Zea mays), 3'ss of exon 1
lower sequence: PP1S56_243V6.3 (Physcomitrella patens), 3'ss of exon 1
-gtgagtcttctcctgctccgtccatc-cgactgcggtgattagaatttga---tccatgggtttgatttagcccctgctttcgcacctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAAGTCCGCG---------
  |  |  |  | ||| |  || ||||  |  | | |||       | |||   |  |||    ||||  ||  | ||  || |  ||  |  |||| || |||||||||||||| ||||| || ||||| ||  ||  | | |||  ||| |||   |||||||||||||| |||||||| |||||||| ||||         
ttttcgggtctttctgttt-gttcatcatggtttcagtgtactttttctgaaatttgatgatgctgatcaaggtcgtgtctt-gttccaat--agtttcaccagTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGA

upper sequence: AC230013.2_FGT007 (Zea mays), 3'ss of exon 1
lower sequence: PP1S56_243V6.2 (Physcomitrella patens), 3'ss of exon 1
-gtgagtcttctcctgctccgtccatccgactgcggtgattagaatttgatccat---gggtttgat----ttagcccctgc--tttcgcacctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAAGTCCGCG
 | |||| || | | | ||  ||  |  |       || ||  | | |  |   |      ||||||     |   |   |   | ||          |||| || |||||||||||||| ||||| || ||||| ||  ||  | | |||  ||| |||   |||||||||||||| |||||||| |||||||| ||||
tgggagtttttttcgggtctttctgtttgttcatcatggtttcagtgtactttttctgaaatttgatgatgctgatcaaggtcgtgtcttgttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCG

upper sequence: AC230013.2_FGT007 (Zea mays), 3'ss of exon 1
lower sequence: PP1S74_193V6.2 (Physcomitrella patens), 3'ss of exon 1
-----gtgagtcttctcctgctccgt----ccatccgac-tgcggtgattagaatttg--atccatgggtttgatttagcccctgctttcgcacctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAAGTCCGCG
      ||| | ||      | ||||      | ||  | |||||| | | |  ||    ||     ||||    |  || ||   ||       | | ||||| ||||| ||||||||||| ||||| || || || ||  |   | | |||   || |||   |||||||||||||||||||||||||||||||| ||||
tgtgtatgattgtttgatgtcaccgtagtatgacccatcatgcggtaacttgttttcatcattttccggttctgatc-gctccaatttcttttggtat-cagTTTCATCAATACCAGGTGGTTGGGCGGGCCCTTCCTACCGCGACCAATGAGACACCTAAGGCTTACCGCATGAAGCTCTGGGCCACCAACGAAGTGCGCG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|15100313|gb|BI396104.1|BI396104
EST:     ATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
genomic: ATGGTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
EST: gi|211263956|gb|FL049653.1|FL049653
EST:     ATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
genomic: ATGGTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
EST: gi|18384240|gb|BM417439.1|BM417439
EST:     ATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
genomic: ATGGTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
EST: gi|29130285|gb|CB380989.1|CB380989
EST:     ATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
genomic: ATGGTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
EST: gi|5343072|gb|AI795482.1|AI795482
EST:     ATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
genomic: ATGGTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
EST: gi|31405721|gb|CD484453.1|CD484453
EST:     ATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
genomic: ATGGTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
EST: gi|211261516|gb|FL049632.1|FL049632
EST:     ATGGTGGCCTTCARG                         TTCCATCAGTACCASGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
genomic: ATGGTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
EST: gi|9794359|gb|BE552667.1|BE552667
EST:     ATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
genomic: ATGGTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
EST: gi|5398753|gb|AI812218.1|AI812218
EST:     ATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
genomic: ATGGTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
EST: gi|211259082|gb|FL049626.1|FL049626
EST:     ATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
genomic: ATGGTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
EST: gi|89757074|gb|DY686828.1|DY686828
EST:     ATGGTGGCCTTCCGG                         TTCCATCCGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
genomic: ATGGTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
EST: gi|31358983|gb|CD443340.1|CD443340
EST:     ATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
genomic: ATGGTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
EST: gi|20301341|gb|BQ164284.1|BQ164284
EST:     ATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
genomic: ATGGTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
EST: gi|14997079|gb|BI319157.1|BI319157
EST:     ATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGG-GGGGCGCGCGCTGCCGACGCCCGGCGACGAG
genomic: ATGGTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
EST: gi|211263947|gb|FL049644.1|FL049644
EST:     ATGGTGGCCTTCAGG                         TTCCATCAGTACCAGGTGGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGA
genomic: ATGGTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGT-GGTGGGGCGCGCGCTGCCGACGCCCGGCGACGA
EST: gi|22542281|gb|BU092719.1|BU092719
EST:     GTGGCCTTCAGG                         TTCCATCAGTACCAGG-GGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG
genomic: GTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 718

ATGGTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAAGTCCGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 495

ATGGTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAAGTCCGCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 472

ATGGTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAAGTCCGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 345

ATGGTGGCCTTCAGGgtgagtcttc ... acctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAAGTCCGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattagaatttgatccatgggtttgatttagcccctgctttcgcacctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAAGTCCGCG
                     gtttgat  putative branch site (score: 345)
                      tttgattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcttctcctgctccgtccatccgactgcggtgattagaatttgatccatgggtttgatttagcccctgctttcgcacctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAAGTCCGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC