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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtcgccatctacatcatcattttgttgagtaatttcataattctctgtcgatattaggtatttcccttgtcaaagctgttcatggttctaataattattttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAG

Basic information

species Zea mays
transcript GRMZM2G037200_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037200_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g45480.4 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------------------gttagtcgccatctacatc--atcattttgttgagtaatttcataattctctgtcgatattaggtatttcccttgtcaaagctgttcatggttctaataattattttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAG
                                                                          ||  | ||  |  |||     ||||||||||   |  | |  |||     | ||  || |     |||  | | |||  ||  |||||  |||||     | |||     ||||||||||| |||||||| ||||||| ||| |||||||||||||||||||||||||| || 
gttagtctctgtccttgactttatgttgtttaataattttgcagatatgtcttcacattccatatcttacccttttcattgcatttcacactcgttcattttgttcc-tgttcttctaacatcatatctgtaatcacgttttatcctttcagtgc-attcatacttctacgctgtgtttctcttcagGTTTGGGCAGCTACAGAAAGTGGAAGCTTGGAAGTAACATATACACACAAAGAGGAGCAT

upper sequence: GRMZM2G037200_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT4G25440.1 (Arabidopsis thaliana), 3'ss of exon 7
gttagtcgccatctacatcatcattttgttgagtaatttcataattctctgtcgatattaggtatttcccttgtcaaagctgttcatggttctaataattattttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAG
           | |   ||   |  | | |   |||||   |   |  |||   ||||  |  ||| |||         |||||  |  || |  |  || ||  |  | || | ||||| ||||| ||  |||||||||||||||| |||||||| |||||||| ||  | 
----------gtttggttc--taactcgctagataattggctcgattcctg--aatat--gacattacccc--------ctgttt-tttttttttttttttttccgttgtagATATGGGCTGCTACTGAAGGTGGAAACTTAGAAGTGACATATACTCACAAAGAAGAATAC
















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|60345951|gb|DN212924.1|DN212924
EST:     TTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAA                         GTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
genomic: TTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAAgttagtcgcc ... tttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
EST: gi|6020641|gb|AW065674.1|AW065674
EST:     TTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAA                         GTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
genomic: TTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAAgttagtcgcc ... tttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
EST: gi|95107946|gb|EB740175.1|EB740175
EST:     TTGCTGGGATCAATTTCTATTATCTTGCTCTTTGCGATCAAACAATAAAA                         GTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACCCAAA
genomic: TTGCTGGGATCAATTTCTATTATCTTGCTCTTTG-GATCAAACAATAAAAgttagtcgcc ... tttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
EST: gi|29576813|gb|CB616925.1|CB616925
EST:     GGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAA                         GTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
genomic: GGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAAgttagtcgcc ... tttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
EST: gi|149070981|gb|EE159386.2|EE159386
EST:     TTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAA                         GTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
genomic: TTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAAgttagtcgcc ... tttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
EST: gi|149086360|gb|EE175901.2|EE175901
EST:     TTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAA                         GTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
genomic: TTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAAgttagtcgcc ... tttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
EST: gi|50334152|gb|CO529278.1|CO529278
EST:     TTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAA                         GTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
genomic: TTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAAgttagtcgcc ... tttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
EST: gi|149095549|gb|EE181206.2|EE181206
EST:     TGCTCTTTGGATCAAACAATAAAA                         GTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
genomic: TGCTCTTTGGATCAAACAATAAAAgttagtcgcc ... tttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
EST: gi|60344000|gb|DN210973.1|DN210973
EST:     TTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAA                         GTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
genomic: TTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAAgttagtcgcc ... tttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
EST: gi|88751062|gb|DY535203.1|DY535203
EST:     TTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAA                         GTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
genomic: TTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAAgttagtcgcc ... tttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
EST: gi|78074602|gb|DV503036.1|DV503036
EST:     TTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAA                         GTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
genomic: TTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAAgttagtcgcc ... tttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
EST: gi|71297927|gb|DR784933.1|DR784933
EST:     TTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAA                         GTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA
genomic: TTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAAgttagtcgcc ... tttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAA

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), 46 (downstream exon)
Score: 127

GCAGTGCATACAGACTCTTTCTGATCATACCGATGTTGTTATGTCCGTGCTTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAAgttagtcgcc ... tttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 91

GCAGTGCATACAGACTCTTTCTGATCATACCGATGTTGTTATGTCCGTGCTTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAAgttagtcgcc ... tttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 107

GCAGTGCATACAGACTCTTTCTGATCATACCGATGTTGTTATGTCCGTGCTTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAAgttagtcgcc ... tttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

GCAGTGCATACAGACTCTTTCTGATCATACCGATGTTGTTATGTCCGTGCTTTGCTGGGATCAATTTCTATTATCTTGCTCTTTGGATCAAACAATAAAAgttagtcgcc ... tttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaggtatttcccttgtcaaagctgttcatggttctaataattattttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAG
                                ttctaat  putative branch site (score: 96)
                                         ttatttt  putative PPT
                                ttctaataattatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtcgccatctacatcatcattttgttgagtaatttcataattctctgtcgatattaggtatttcccttgtcaaagctgttcatggttctaataattattttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT