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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgagcgatctggcccgattcggactcgagggttttgatttggtttctctgatcgagtgtgttctgctcgtcgcgtgcgtgcgtgctgctgctgctgcttcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGCGCTGGACAAGGCCACCAACGAGACGATCGCGCTCAAGAAGATCCGCC

Basic information

species Zea mays
transcript GRMZM2G008327_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g02680.2 (Oryza sativa), 3'ss of exon 1
gtaagcg-----agcgatctggcccgattcggactcgagggttttgatttggtttctctgatcgagtgtgt-tctgctcg---tcgcgtgcgtgcgtgctgctgctgctgctt-cagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGCGCTGGACAAGGCCACCAACGAGACGATCGCGCTCAAGAAGATCCGCC
|| ||||     |||||||||   |||||     ||  |||    || | ||    | |||||  |      | |||| |   | | |   ||| |||| || |  || |    ||||||||||||| ||||||||| |||||||||||||||||||||||||||| ||||| |||||||| ||||||||||||||||||||||||||||||||| |
gtgagcgcctcgagcgatctgattcgatttctgttcttgggg---gactcgggggttttgatcctgcaaacctttgcttgtttttgtggctgtgtgtgcggcgggggcggggcgcagTACGAGAAGGAGGAGAAGATTGGGGAGGGCACGTACGGGGTGGTGTACAGGGCGCGGGACAAGGTCACCAACGAGACGATCGCGCTCAAGAAGATCCGGC

upper sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 1
gtaagcgagcgatctggcccgattcggactcgagggttttgatttggtttctctgatcgagtgtgttctgctcgtcgcgtgcgtgcgtgctgctgctgctgcttcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGCGCTGGACAAGGCCACCAACGAGACGATCGCGCTCAAGAAGATCCGCC---
                    |     |  || || | | ||||| | || ||||  | | | |       ||||    | |  |   | ||||     |   | ||||||||| |||   ||||||| || ||||||||||||||||| ||||||||||||| |||||||| ||||||||||||||||||||||||||||||||| |   
--------------------gtaagcgcttccagcgatctgattcgattcctcttcttggggg------actcg----gggttttgatcctgcaa--acctttgcagTACGAGGAGG---AGAAGATTGGAGAGGGCACGTACGGGGTAGTGTACAAGGCGCGGGACAAGGTCACCAACGAGACGATCGCGCTCAAGAAGATCCGGCTTG

upper sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA15G14390.1 (Glycine max), 3'ss of exon 1
gtaagcgagcgatctggcccgattcggactcgagggttttgatttggtttctctgatcgagtgtgttctgctcgtcgcgtgcgtgcgtgctgctgctgctgcttcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGCGCTGGACAAGGCCACCAACGAGACGATCGCGCTCAAGAAGATCCGCC
||  |  |||         | ||     |||   | |||| | ||   |      | |     | |  ||    | | ||    |  |  |     |  |  | ||||||||||||||||||||||| || ||||| || ||||| || || |||||||| |  |||   | |||||| ||||| ||||| ||||||||||| ||||
gttcgt-agcaccgcaatgc-atcatctctcttcgattttcagtttcctctcaaaaactcacttttcgtgaaaattg-gttttcgatttttttgtttttttttgcagTACGAGAAGGTGGAGAAGATAGGCGAGGGAACATACGGCGTCGTTTACAAGGCTCGCGACCGCGTCACCAATGAGACCATCGCTCTCAAGAAGATTCGCC

upper sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G03470.1 (Glycine max), 3'ss of exon 1
gtaagcgagcgatctggcccgattcggactcgagggttttgatttggtttctctgatcgagtgtgttctgctcgtcgcgtgcgtgcgtgctgctgctgctgctt-cagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGCGCTGGACAAGGCCACCAACGAGACGATCGCGCTCAAGAAGATCCGCC
    |              | ||    |||  |     || |  |  | |      |  | | |  |||      | |     | | | |   |  |  |  || ||||||||||||||||||||||| || ||||| || ||||| || || |||||||| |  |||   |||||||| ||||| ||||| || |||||||| ||||
----gttcctaccacaattcaatcttaacttcatcacattaacattttcttcgattttcactttcctctcacaaactcacttttcctttccattttttttttttgcagTACGAGAAGGTGGAGAAGATAGGCGAGGGAACATACGGCGTCGTTTACAAGGCTCGCGACCGCGCCACCAATGAGACAATCGCTCTGAAGAAGATTCGCC

upper sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S281_23V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaagcgagcgatctggcccgattcggactcgagggttttgatttggtttctctgatcgagtgtgttctgctcgtcgcgtgcgtgcgtgctgctgctgc--tgcttcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGCGCTGGACAAGGCCACCAACGAGACGATCGCGCTCAAGAAGATCCGCC
        || |||   |   |  | | |||     |||  |||  ||  |   |  |  ||||      | |        | ||      ||  |||   ||   ||||| || || ||||||||||| ||||| |||| |||||| |||||||||||||| |  |||   |  ||||| ||||| || || || ||||||||  | |
------ttgctatccatcttcaaactgtctc---attttacattctgtgacgaagcccatgtgtcactcacccaatctcctcttgatgatggcaactgtaatgtggcagTATGAAAAAGTGGAGAAGATTGGGGAAGGCATGTACGGAGTGGTGTACAAGGCCCGAGACCGCGTTACCAATGAGACTATTGCTCTAAAGAAGATTAGGC

upper sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ15022 (Selaginella moellendorffii), 3'ss of exon 1
gtaagcgagcgatctggcccgattcggact-cgagggttt-tgatttggtttctctgatcgagtgtgttctgctcgtcgcgtgcgtgcgtgctgctgctgctgcttcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGCGCTGGACAAGGCCACCAACGAGACGATCGCGCTCAAGAAGATCCGCC
                         | ||| ||| |     |  || | | |||||  |       | |||| || |   || | |||  ||| ||   |  || | |||| |||||||||||||| |||||||| ||||| ||||| || || |||||||| | |||      ||| || |||||||| ||||||||||||||||| |
-------------------------gtactgcgaagccgcattcttcgatctctctcgttcttgccgctctgatcttactgttcttgc--gcttcttgcggcgcgt-agTATGAGAAGGTGGAGAAAATCGGGGAAGGCACATACGGCGTCGTCTACAAGGCCCGGGATCGCATCACAAATGAGACGATTGCGCTCAAGAAGATCCGAC

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|61119625|gb|DN560586.1|DN560586
EST:     CGCACCCGCAGCCGCGGCCGCGTTCGCATTGGGGGCACGCAATGGAGCAG                         TACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAG
genomic: CGCACCCGCAGCCGCGGCTGCGTTCGCATTGGGGGCACGCAATGGAGCAGgtaagcgagc ... gctgcttcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAG
EST: gi|87152029|gb|DY396818.1|DY396818
EST:     GGGGCACGCAATGGAGCAG                         TACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAG
genomic: GGGGCACGCAATGGAGCAGgtaagcgagc ... gctgcttcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAG
EST: gi|22542942|gb|BU093380.1|BU093380
EST:     CGCACCCGCAGCCGCGGCCGCGTTCGCATCGGGGCCACGCAATGGAGCAG                         CACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAG
genomic: CGCACCCGCAGCCGCGGCTGCGTTCGCATTGGGGGCACGCAATGGAGCAGgtaagcgagc ... gctgcttcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAG
EST: gi|93281356|gb|EB673620.1|EB673620
EST:     CGCACCCGCAGCCGCGGCTGCGTTCGCATTGGGGGCACGCAATGGAGCAG                         TACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAG
genomic: CGCACCCGCAGCCGCGGCTGCGTTCGCATTGGGGGCACGCAATGGAGCAGgtaagcgagc ... gctgcttcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAG

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: 154

CTCCACCCCACCCCGCTCCCGCTTCCGCTTCCTCGCCACTTAGTTCGTTCCGCACCCGCAGCCGCGGCTGCGTTCGCATTGGGGGCACGCAATGGAGCAGgtaagcgagc ... gctgcttcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGCGCTGGACAAGGCCACCAACGAGACGATCGCGCTCAAGAAGATCCGCC


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 54

CTCCACCCCACCCCGCTCCCGCTTCCGCTTCCTCGCCACTTAGTTCGTTCCGCACCCGCAGCCGCGGCTGCGTTCGCATTGGGGGCACGCAATGGAGCAGgtaagcgagc ... gctgcttcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGCGCTGGACAAGGCCACCAACGAGACGATCGCGCTCAAGAAGATCCGCC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 67

CTCCACCCCACCCCGCTCCCGCTTCCGCTTCCTCGCCACTTAGTTCGTTCCGCACCCGCAGCCGCGGCTGCGTTCGCATTGGGGGCACGCAATGGAGCAGgtaagcgagc ... gctgcttcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGCGCTGGACAAGGCCACCAACGAGACGATCGCGCTCAAGAAGATCCGCC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 33

CTCCACCCCACCCCGCTCCCGCTTCCGCTTCCTCGCCACTTAGTTCGTTCCGCACCCGCAGCCGCGGCTGCGTTCGCATTGGGGGCACGCAATGGAGCAGgtaagcgagc ... gctgcttcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGCGCTGGACAAGGCCACCAACGAGACGATCGCGCTCAAGAAGATCCGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatcgagtgtgttctgctcgtcgcgtgcgtgcgtgctgctgctgctgcttcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGCGCTGGACAAGGCCACCAACGAGACGATCGCGCTCAAGAAGATCCGCC
 ctctgat  putative branch site (score: 33)
                                              ctgcttc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgagcgatctggcccgattcggactcgagggttttgatttggtttctctgatcgagtgtgttctgctcgtcgcgtgcgtgcgtgctgctgctgctgcttcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGCGCTGGACAAGGCCACCAACGAGACGATCGCGCTCAAGAAGATCCGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG