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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttttacatggtcatggtcaaaacattctctcgcagttttcatatacaacgactaagatcaatttctgcaaatattttagttttgaatatctctgcaccttgtctccttaacctgctgcactcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGTCCGTCCACCAGCCAATGGCAACAGCGGGTCTGGTGTGTTTAGAGGAAGA

Basic information

species Zea mays
transcript GRMZM2G117388_T04
intron # 6
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117388_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g09550.3 (Oryza sativa), 3'ss of exon 5
gtatccttt--tacatgg--tcatggtcaaaacattctctcgcagttttcatatacaacgactaagatcaatttctgcaaatattttagttttgaatatctctgcaccttgtctccttaacctgctgcactcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGTCCGTCCACCAGCCAATGGCAACAGCGGGTCTGGTGTGTTTAGAGGAAGA---
|||||||||  || ||||  |||||| |||| ||||      || |               | | | |||||  || | | || | || ||| ||   |    || || ||  ||||||||         |  || |||||||||||||||||||||||||||| |||||  |||| |||||| | || ||||| ||  | |||   | ||||| ||| || || |  || ||||||||    
gtatccttttttatatgggttcatggccaaagcattt-----caat---------------ccatgttcaatagctactactactatattttcgatggtacacgctccatggttccttaac---------tgctgtacagACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGTCCGACCCGCGGCC---GCCAACACCGGATCAGGCGCCTTCAGAGGAAGGAGC
















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|161590672|gb|EY958674.1|EY958674
EST:     CGGGAAGAGCTACCTCAAGACTCCTAAATGGGT                         ACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
genomic: CGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
EST: gi|211265389|gb|FL116395.1|FL116395
EST:     TTGCACCCTCTTGCCACCGGGAAGAACTACCTCAAGACTCCTAAATGGGT                         ACATAAGATTGTTTCTCGATTCAGGATAGGCATGCAAGCAAACTCACCCGT
genomic: TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
EST: gi|60397359|gb|DN230175.1|DN230175
EST:     TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGT                         ACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
genomic: TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
EST: gi|21331882|gb|BQ487263.1|BQ487263
EST:     TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGT                         ACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
genomic: TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
EST: gi|7135572|gb|AW498154.1|AW498154
EST:     TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAAT-GG-                         ACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
genomic: TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
EST: gi|211211598|gb|FL477381.1|FL477381
EST:     TTGCACCCTCTTGCCACCGGGAAGAACTACCTCAAGACTCCTAAATGGGT                         ACATAAGATTGTTTCTCGATTCAGGATAGGCATGCAAGCAAACTCACCCGT
genomic: TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
EST: gi|211211597|gb|FL477380.1|FL477380
EST:     TTGCACCCTCTTGCCACCGGGAAGAACTACCTCAAGACTCCTAAATGGGT                         ACATAAGATTGTTTCTCGATTCAGGATAGGCATGCAAGCAAACTCACCCGT
genomic: TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
EST: gi|40336279|gb|CK370349.1|CK370349
EST:     TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGT                         ACATAAGATTGTTGCTCGATTCAAGATAGGCATGCAAGCGAACTCACCCGT
genomic: TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
EST: gi|60349033|gb|DN216006.1|DN216006
EST:     TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGT                         ACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
genomic: TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
EST: gi|211191572|gb|FL254972.1|FL254972
EST:     TACCTCAAGACTCCTAAATGGGNTT                         ACATAAGATTGTTTCTCGATTCAGGGATAGGCATGC
genomic: TACCTCAAGACTCCTAAATGGG-T-gtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGG-ATAGGCATGC
EST: gi|211191572|gb|FL254972.1|FL254972
EST:     TACCTCAAGACTCCTAAATGGGNTT                         ACATAAGATTGTTTCTCGATTCAGGGATAGGCATGC
genomic: TACCTCAAGACTCCTAAATGGG-T-gtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGG-ATAGGCATGC
EST: gi|211211596|gb|FL477379.1|FL477379
EST:     AAGAACTACCTCAAGACTCCTAAATGGGT                         ACATAAGATTGTTTCTCGATTCAGGATAGGCATGCAAGCAAACTCACCCGT
genomic: AAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
EST: gi|211342720|gb|FL460317.1|FL460317
EST:     TTGCACCCTCTTGCCACCGGGAAGAACTACCTCAAGACTCCTAAATGGGT                         ACATAAGATTGTTTCTCGATTCAGGATAGGCATGCAAGCAAACTCACCCGT
genomic: TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
EST: gi|71767311|gb|DR965248.1|DR965248
EST:     TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGT                         ACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
genomic: TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
EST: gi|211342721|gb|FL460318.1|FL460318
EST:     TTGCACCCTCTTGCCACCGGGAAGAACTACCTCAAGACTCCTAAATGGGT                         ACATAAGATTGTTTCTCGATTCAGGATAGGCATGCAAGCAAACTCACCCGT
genomic: TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
EST: gi|211191573|gb|FL254973.1|FL254973
EST:     TTGCACCCTCTTGCCACCGGGAAGAACTACCTCAAGACTCCTAAATGGGT                         ACATAAGATTGTTTCTCGATTCAGGATAGGCATGCAAGCAAACTCACCCGT
genomic: TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
EST: gi|7135238|gb|AW497985.1|AW497985
EST:     TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAAT-GG-                         ACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
genomic: TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
EST: gi|67030179|gb|CO458928.1|CO458928
EST:     TTGCACCCTCTTGCCACCGGGAAGAACTACCTCAAGACTCCTAAATGGGT                         ACATAAGATTGTTTCTCGATTCAGGATAGGCATGCAAGCAAACTCACCCGT
genomic: TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
EST: gi|16927150|gb|BM080219.1|BM080219
EST:     TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGT                         ACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
genomic: TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
EST: gi|166531613|gb|EG309021.1|EG309021
EST:     TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGG-T                         ACATAAGATTGTTGC
genomic: TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGC
EST: gi|37392930|gb|CF633718.1|CF633718
EST:     TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGT                         ACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT
genomic: TTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGT

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 31 (downstream exon)
Score: 17

CTGGACTTCTGGGTATCATGGTTGGACATCTCTACTACTTCTTTGCAGTGTTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGTCCGTCCACCAGCCAATGGCAACAGCGGGTCTGGTGTGTTTAGAGGAAGA


Block sizes: 49 (upstream exon), 32 (downstream exon)
Score: 5

CTGGACTTCTGGGTATCATGGTTGGACATCTCTACTACTTCTTTGCAGTGTTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGTCCGTCCACCAGCCAATGGCAACAGCGGGTCTGGTGTGTTTAGAGGAAGA


Block sizes: 49 (upstream exon), 32 (downstream exon)
Score: 30

CTGGACTTCTGGGTATCATGGTTGGACATCTCTACTACTTCTTTGCAGTGTTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatcctttt ... tcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGTCCGTCCACCAGCCAATGGCAACAGCGGGTCTGGTGTGTTTAGAGGAAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagttttgaatatctctgcaccttgtctccttaacctgctgcactcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGTCCGTCCACCAGCCAATGGCAACAGCGGGTCTGGTGTGTTTAGAGGAAGA
 ctccttaac  putative branch site 
                                          cactctt  putative PPT
     tttgaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccttttacatggtcatggtcaaaacattctctcgcagttttcatatacaacgactaagatcaatttctgcaaatattttagttttgaatatctctgcaccttgtctccttaacctgctgcactcttgcacagACATAAGATTGTTGCTCGATTCAGGATAGGCATGCAAGCGAACTCACCCGTCCGTCCACCAGCCAATGGCAACAGCGGGTCTGGTGTGTTTAGAGGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA