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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgtaccagactaccaccagtcttcaacaatgacatctattaactaactacatatcttttcatatcgaaaacatgttgaggtttctgctgtcttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATGTTTGTAGTTGGAGTTAATGAGAATAGCTATGATCCAAAGATGAATGTTG

Basic information

species Zea mays
transcript GRMZM2G104632_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 7
gtttgtgtaccagactac-caccagtcttcaacaatgacatcta-ttaactaactacatatcttttcatatcgaaaacatgttgaggtttctgctgtcttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATGTTTGTAGTTGGAGTTAATGAGAATAGCTATGATCCAAAGATGAATGTTG
            |  |   ||||| |  |  ||| || ||||||  | |  ||   ||    |||  || | || || ||| ||| |||| |  || ||| |||  |||| ||||| |||||||| ||||||||||| |||||||| |||||||| |||||||| |||||||| |||||||| ||||||||||| || ||||||||||
------------gtttgtacaccatttctatacattgccatctaactgagaaatggcaagcttttatat-tggataaaatggtgatgttttta-tgccttgtttgtagGGCGGTGCTAAGAAAGTTGTGATATCTGCTCCATCAGCAGATGCTCCAATGTTTGTCGTTGGAGTAAATGAGAAGAGCTATGATCCTAAAATGAATGTTG

upper sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT1G16300.1 (Arabidopsis thaliana), 3'ss of exon 7
--------------------------gtttgtgtaccag----actaccaccagtcttcaacaatga--catctatta--actaactacatatcttttcatatcgaaaacatgt-tgaggtttctgctgtcttatt-----tacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATGTTTGTAGTTGGAGTTAATGAGAATAGCTATGATCCAAAGATGAATGTTG
                          |||  | ||| ||    | |    | |   || || |   |  | | |||||  | ||| | || |  ||    |    |||   | | |||  ||  ||   | | |||     | ||||||||||| ||||| ||  | || |||||||| ||||| || || ||||||||||| |||||||| ||||| || |  ||    || || ||| || | |
gtatgcactttcatttgaacacgcttgttgatctactagtttcattgatgctaacatttaataccaagccttatattattaataattccaaacattcaactcctaaaatggtctatgattttcttgacctttcattgtctgtgcagGGTGGTGCTAAGAAGGTCATCATTTCTGCACCTTCAGCGGACGCGCCCATGTTTGTTGTTGGAGTAAATGAAAAGACATACCTGCCTAACATGGATATAG

upper sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv19s0085g00600.t01 (Vitis vinifera), 3'ss of exon 7
gtttgtgtaccagactaccaccagtcttcaacaatgacatctattaactaactacatatcttttcatatcgaaaacatgttgaggtttctgctgtcttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATGTTTGTAGTTGGAGTTAATGAGAATAGCTATGATCCAAAGATGAATGTTG
||| || |   | | |          ||  |  |   | ||||   |||  ||    | |      |   |||  ||    | | ||   |   |  || |  ||||||||||| ||||||||||| || || || |||||||||||||| || |||||||| || ||||| ||||||| |   ||  | ||||  |||||| |||
gttcgt-tggtata-tgttgtggactttatattagttcttctaaacactctcttgccaccccactgtgctgaagtca----gtgattgtcgtctttataat-gcagGGTGGTGCCAAGAAAGTGGTAATTTCAGCTCCATCAGCTGATGCACCGATGTTTGTGGTAGGAGTAAATGAGACTTCATACAAGCCAAGCATGAATATTG

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|29576993|gb|CB617105.1|CB617105
EST:     AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAG                         GGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
genomic: AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAGgtttgtgtac ... ttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
EST: gi|60397796|gb|DN230612.1|DN230612
EST:     AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAG                         GGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
genomic: AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAGgtttgtgtac ... ttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
EST: gi|211318619|gb|FL124696.1|FL124696
EST:     AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAG                         GGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
genomic: AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAGgtttgtgtac ... ttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
EST: gi|211011830|gb|FL066256.1|FL066256
EST:     AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAG                         GGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
genomic: AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAGgtttgtgtac ... ttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
EST: gi|67017162|gb|CO445911.1|CO445911
EST:     AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAG                         GGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
genomic: AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAGgtttgtgtac ... ttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
EST: gi|211009063|gb|FL066254.1|FL066254
EST:     AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAG                         GGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
genomic: AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAGgtttgtgtac ... ttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
EST: gi|21088933|gb|BQ401246.1|BQ401246
EST:     AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAG                         GGTGGTGCAAAGAAAGGGGTGATATCTGCACCATCAGCTGATGCTCCCATG
genomic: AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAGgtttgtgtac ... ttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
EST: gi|6564069|gb|AW231691.1|AW231691
EST:     AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAG                         GGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
genomic: AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAGgtttgtgtac ... ttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
EST: gi|28987666|gb|CB351748.1|CB351748
EST:     AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAG                         GGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
genomic: AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAGgtttgtgtac ... ttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
EST: gi|24769367|gb|CA404496.1|CA404496
EST:     AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAG                         GGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
genomic: AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAGgtttgtgtac ... ttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
EST: gi|5928870|gb|AW056162.1|AW056162
EST:     AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAG                         GGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
genomic: AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAGgtttgtgtac ... ttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
EST: gi|91869745|gb|EB400519.1|EB400519
EST:     AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAG                         GGTGGTGCCAAGAAAGTGGTGAT
genomic: AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAGgtttgtgtac ... ttatttacagGGTGGTGCAAAGAAAGTGGTGAT
EST: gi|211011829|gb|FL066255.1|FL066255
EST:     AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAG                         GGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG
genomic: AATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAGgtttgtgtac ... ttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATG

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: 761

AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAGgtttgtgtac ... ttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATGTTTGTAGTTGGAGTTAATGAGAATAGCTATGATCCAAAGATGAATGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 383

AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAGgtttgtgtac ... ttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATGTTTGTAGTTGGAGTTAATGAGAATAGCTATGATCCAAAGATGAATGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 305

AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAGgtttgtgtac ... ttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATGTTTGTAGTTGGAGTTAATGAGAATAGCTATGATCCAAAGATGAATGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 843

AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAGgtttgtgtac ... ttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATGTTTGTAGTTGGAGTTAATGAGAATAGCTATGATCCAAAGATGAATGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacatatcttttcatatcgaaaacatgttgaggtttctgctgtcttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATGTTTGTAGTTGGAGTTAATGAGAATAGCTATGATCCAAAGATGAATGTTG
                                           tcttattt  CT-rich tract
         ttttcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgtaccagactaccaccagtcttcaacaatgacatctattaactaactacatatcttttcatatcgaaaacatgttgaggtttctgctgtcttatttacagGGTGGTGCAAAGAAAGTGGTGATATCTGCACCATCAGCTGATGCTCCCATGTTTGTAGTTGGAGTTAATGAGAATAGCTATGATCCAAAGATGAATGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG