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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caagttagtttatactagtgcaaccaagtgttgccattagtaattattatggcatttttttttctttctggaataataattgtttgacgattggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG

Basic information

species Zea mays
transcript GRMZM2G110834_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g02890.1 (Oryza sativa), 3'ss of exon 10
-------caagttagtttatactagtgcaaccaagtgttgccattagtaattattatggcatttttttttctttctggaataataattgtttgacgattggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG
       | |  |   |  |   | |   | |||          ||  | ||   |  | |||  |     ||  |   ||||   |||| |||    || || ||| |||||  ||||||||||||| || ||||| ||||||||||| ||||| |||||| ||||||| ||| | ||||||||||||||||| |
cagcattctaactgcatgcttacaataggatcaaacagcttggctataagtt--cacagaattcatacccattaataatataac--ttgtctgaa---tgattgcagGAAACCTGTTAAAAAGGTGGGGTCTTTCTGTTGGCTTTCCCTAGCTATTTGCATTTTGGAGCTTCTACTATGCATCAAGTTTGGACATG

upper sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 10
lower sequence: AT1G15110.2 (Arabidopsis thaliana), 3'ss of exon 11
caagttagtttatactagtgcaaccaagtgttgccattagtaattattatggcatttttttttctttctggaataataattgtttgacgattggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG----
         | |  |||  || ||   | | |     | | | ||| | ||| |    |||   | | |  ||      | ||||   | ||| |  ||| |||||  | |||||||||||| | ||||| ||||| || ||||  |||||||| || || || || ||||||||||||||||||   |    
--------gtaaagctatagccact--gcgatattggttggagttagtttggaaagagttt---tgtatataacttgtgtagttt--tggttgttcacagAAAACCTGTGAAAAAGGTGGGAGCATTCTGTTGGCTGTCACTGGGGATATGCATAGTAGAACTTCTCATCTGCATCAAGTTTGGAAGTGGTAG

upper sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 10
lower sequence: AT1G15110.1 (Arabidopsis thaliana), 3'ss of exon 11
caagttagtttatactagtgcaaccaagtgttgccattagtaattattatggcatttttttttctttctggaataataattgtttgacgattggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG
         | |  |||  || ||   | | |     | | | ||| | ||| |    |||   | | |  ||      | ||||   | ||| |  ||| |||||  | |||||||||||| | ||||| ||||| || ||||  |||||||| || || || || ||||||||||||||||||   |
--------gtaaagctatagccact--gcgatattggttggagttagtttggaaagagttt---tgtatataacttgtgtagttt--tggttgttcacagAAAACCTGTGAAAAAGGTGGGAGCATTCTGTTGGCTGTCACTGGGGATATGCATAGTAGAACTTCTCATCTGCATCAAGTTTGGAAGTG

upper sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 11
------------------------caagt----tagtttatactagtgcaaccaagtgttgccattagtaattattatggcatttttttttctttctggaataataattgtttgacgattggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG
                        ||| |    || || ||||||      ||||       |||||||    || || |      |||||||| |     |  ||| ||||      ||   ||||| |||||| | |||||||||||| | || || ||||||||||| ||||| |||||| | || || || || ||||||||||||||||| |
gtactatctctccttgcttatttgcaaatattatacttgatactaagaatgccaa---ccagcattagtgtgcat-atagttcaaatttttcttac-attttggtaaatgttgtgtcgtt--cttcagAAAACCAGTGAAAAAGGTGGGAGCGTTTTGTTGGCTTTCCCTTGCTATTTGCATTATTGAACTACTCATTTGCATCAAGTTTGGACATG

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|42491818|gb|CK700864.1|CK700864
EST:     TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAG                         CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATG
genomic: TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAGgtataatttc ... ttggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATG
EST: gi|60397677|gb|DN230493.1|DN230493
EST:     TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAG                         CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATG
genomic: TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAGgtataatttc ... ttggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATG
EST: gi|91869156|gb|EB400279.1|EB400279
EST:     TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAG                         CAAACCATTTAAAAAGGTGGGATCCTTTTGCTGGCTTTCCCTGGCTATATG
genomic: TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAGgtataatttc ... ttggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATG
EST: gi|84969395|gb|DW467833.1|DW467833
EST:     TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAG                         CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATG
genomic: TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAGgtataatttc ... ttggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATG
EST: gi|211076057|gb|FL474784.1|FL474784
EST:     TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAG                         CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATG
genomic: TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAGgtataatttc ... ttggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATG
EST: gi|6672167|gb|AW282342.1|AW282342
EST:     TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAG                         CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATG
genomic: TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAGgtataatttc ... ttggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATG
EST: gi|74231927|gb|DT639841.1|DT639841
EST:     TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAG                         CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATG
genomic: TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAGgtataatttc ... ttggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATG
EST: gi|71318559|gb|DR796040.1|DR796040
EST:     TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAG                         CAAACCATTTAAAAAGGTGGGATCCTTTTGCTGGCTTTCCCTGGCTATATG
genomic: TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAGgtataatttc ... ttggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATG
EST: gi|76910092|gb|DV163696.1|DV163696
EST:     TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAG                         CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATG
genomic: TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAGgtataatttc ... ttggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATG
EST: gi|211529174|gb|FL238578.1|FL238578
EST:     TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAG                         CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATG
genomic: TTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAGgtataatttc ... ttggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATG

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: 47 (upstream exon), 42 (downstream exon)
Score: 50

GGATCCCTCCGCGGAACCCCTTGATTGTCTATCGGCTGGTCCTTTGGTGGTTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAGgtataatttc ... ttggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 32

GGATCCCTCCGCGGAACCCCTTGATTGTCTATCGGCTGGTCCTTTGGTGGTTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAGgtataatttc ... ttggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 53

GGATCCCTCCGCGGAACCCCTTGATTGTCTATCGGCTGGTCCTTTGGTGGTTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAGgtataatttc ... ttggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 40

GGATCCCTCCGCGGAACCCCTTGATTGTCTATCGGCTGGTCCTTTGGTGGTTAATCGCGATACCAACCATCCGCGAGTACAATACCTACTTGCAAGACAGgtataatttc ... ttggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatggcatttttttttctttctggaataataattgtttgacgattggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG
                                    gtttgac  putative branch site (score: 40)
        atttttttttctttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caagttagtttatactagtgcaaccaagtgttgccattagtaattattatggcatttttttttctttctggaataataattgtttgacgattggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - caaccaa
- - - - - - - - - - - - - - tgttgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtttg