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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctacttggggccatctgaatctgtcgggaatctgataggggcaagtctgcagtttagctgaccattttgttgtctaatgcatgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT

Basic information

species Zea mays
transcript GRMZM2G053868_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053868_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g03410.2 (Oryza sativa), 3'ss of exon 5
-----------------------gtatctac-ttggggccatctgaatctgtcgg--gaatctgataggggcaagtc-tgcagtttagctgaccatt--ttgttgtctaatgcatgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT
                        ||| | | |    || || ||  ||     |  |  ||||||  | | | | | | ||  |  || |  ||||  ||||| |||      | || ||||||| ||||| || || || ||||| ||||| || ||||| |||||||||||  |||||||||||||||| |||||||||||||||||||||||||||||
gtatttatttcaagagcttttgcttatgtgcatctttgctatgtgcttccaattgttgcttctgatttgagtaggacatacaagtctgcagttcattcattgttttctttcat-tactgtagGGAAAAAGTTTCACGATATAGTTGGCAGTGCCTATTATGTAGCACCAGAAGTTTTAAAACGACGGTCTGGCCCTGAGTCAGATGTTTGGAGCATAGGAGT

upper sequence: GRMZM2G053868_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------gtatctacttggggc-----catctgaatctgtcgggaatctgataggggcaagtctgcagttt---------agctgaccattttgttgtctaatgcatgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT
                                                       | | |  ||  |||     |  ||   |||   |   |  |   |||        |||  |||         |  ||    | |   | | | |   |   |  ||| || ||||| ||||| |||||||| |||||||||||||| ||||| |||||  |||||||   |||||||||| | |||||||| ||||| || || ||
gtgagggaaagtcttgatttttgtggtcaatttctttctttttcttttcttccattttttgtttcaggcttgttctcctatttcttcagttgagttatcaggcatgctcttgccatttttatttgagatttgtttttctctatctttgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGTAAGTCTGGTCCTCAATCAGATGTGTGGAGTATTGGTGT

upper sequence: GRMZM2G053868_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G08180.1 (Glycine max), 3'ss of exon 6
--------------------gtatctacttggggccatctgaatctgtcgg-gaatctgataggggca---agtctgcagtttag--ctgaccattttgttgtctaatgcatgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT
                     |   || || |  || | |  |||  ||   | ||   | | |  |    | |||  | || ||   |     || | |    |     |      ||| |||| ||| || || |||||||| |||||||||||||| |||||||||||  ||||||||  ||| ||||| ||||||||||| ||||| || || ||
gtgagcaaaaatatgtgttaatcgttattttgttccctttttatccctctttgcattcaacatgttcttgcaatctttatttgagagttatttgttctctctctttgaaaacaaaacagGAAAGAGGTTTCAAGATATTGTTGGCAGTGCTTACTATGTTGCACCAGAAGTGTTAAAACGAAAGTCAGGTCCCGAGTCAGATGTATGGAGTATTGGTGT

upper sequence: GRMZM2G053868_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA01G37100.1 (Glycine max), 3'ss of exon 6
-------------------gtatctacttggggccatctgaatctgtcg-ggaatctgataggggca---agtctgcagtttagctgaccattttgttgtctaatgcatgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT
                     ||   ||| |   | | |  |||  ||   | ||   | | |  |    | |||  | || || | |   |||| |    |     |      ||| |||| ||| || || |||||||| |||||||||||||| |||||||||||  |||||||   ||| ||||| ||||| ||||| ||||| || || ||
gtgagcaaaaatgtgttgatcattatctttgtttcctttttatccctcttagcattcaaaatgttcttgcaatctttatttgagtt-atggttttctctctttgcaaacaaaacagGAAAGAGGTTTCAAGATATTGTTGGCAGTGCTTACTATGTTGCACCAGAAGTGTTAAAACGTAAGTCAGGTCCCGAGTCGGATGTATGGAGTATTGGTGT

upper sequence: GRMZM2G053868_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------gtatctacttggggccatctgaatctgtcggg--aatctgataggggcaagtctgcagttt-agctga---ccattttgtt--gtctaatgcatgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT
                                                       | | |  |   |||    |  || | |  ||   |  |   | |        || | ||| |  |||     |||||  |   ||| |   |   |  ||| || ||||| ||||| |||||||| |||||||||||||| ||||| |||||  |||||||   ||| |||||| | |||||||| ||||| || || ||
gtgagggaaagtcttgattttcatgctcaatttctttatttttcttttcttccattttttgttgcaggcttgttctatttctttggttgagttatcaagcatgctcttgtaattttatttgagatttatttttctctatctgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGCAAGTCAGGTCCTCAATCAGATGTGTGGAGTATTGGTGT

upper sequence: GRMZM2G053868_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ17487 (Selaginella moellendorffii), 3'ss of exon 4
gtatctacttggggccatctgaatctgtcgggaatctgataggggcaagtctgcagttta-gctgaccattttgttgtctaatgcatgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT
                                       || |  | |  |     | ||     |      |||| || |     |     ||| ||||  ||||||||  |||||||||| || |||||||| ||||| |||||||| ||| ||  |||||| || ||||| |||||||||||  |||| ||
--------------------------------------gtaagcaccacgcattgctctacatcaattcagctgttctccaccttgtctcacagGAAAGAGATTCCATGATGTTGTTGGAAGCGCGTACTATGTAGCACCCGAAGTACTGAAAAGAAAGTCTGGGCCAGAGTCCGATGTTTGGAGTGTAGGTGT

upper sequence: GRMZM2G053868_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ28817 (Selaginella moellendorffii), 3'ss of exon 4
gtatctacttggggccatctgaatctgtcgggaatctgataggggcaagt-ctgcagtttagctgaccattttgttgtctaatgcatgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT
                                     |  ||   || |   |||| |  | |    ||  | ||| || ||    |     ||| ||||  ||||||||  |||||||||| || |||||||| ||||| |||||||| ||| ||  |||||| || ||||| |||||||||||  | || ||
-------------------------------------gtaagcaccacgcattgcactacatcaattcagct-gttctccaacttgtctcacagGAAAGAGATTCCATGATGTTGTTGGAAGCGCGTACTATGTAGCACCCGAAGTACTGAAAAGAAAGTCTGGGCCAGAGTCCGATGTTTGGAGTGTGGGTGT

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: 48 (upstream exon), 49 (downstream exon)
Score: 113

AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgtatctactt ... catgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 241

AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgtatctactt ... catgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 401

AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgtatctactt ... catgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 233

AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAGgtatctactt ... catgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataggggcaagtctgcagtttagctgaccattttgttgtctaatgcatgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT
                                     gtctaat  putative branch site (score: 233)
                             attttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctacttggggccatctgaatctgtcgggaatctgataggggcaagtctgcagtttagctgaccattttgttgtctaatgcatgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA