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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgctggactgctggtggagaagaaagatttgatcttgatgccggattctggttccgtctttgatttgggcggtgctgactccctgttgctgtttcttggccttggttgtggtgaatccag

Basic information

species Zea mays
transcript GRMZM2G052713_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052713_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g10560.1 (Oryza sativa), 5'ss of exon 2
ATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgctggactgctggtggagaagaaagatttgatcttgatgccggattctggttccgtctttgatttgggcggtgctgactccctgttgctgtttcttggccttggttgtggtgaatccag
||||||||||||||||||||||| ||||||||||| || ||||||||||||||||| ||| | ||||||||||| |||||||||||||| ||||||||||||||      ||    |  |   || |||    ||  ||||||  || || |     |   |   || || ||||   |      ||   || || |                             
ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAGTACTACGTCCCGCTCGAGGACTCGGAGAAGCACAAGGTCGAGTACGAGgtgag------ggggatccagcaaaggaga----ttccatcttggcgctggttcgatttgtgggtgttcatctgggtctt-----ttcttggtcgcag-----------------------------

upper sequence: GRMZM2G052713_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA17G37730.1 (Glycine max), 5'ss of exon 2
ATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgctggactgctggtggagaagaaagatttgatcttgatgccggattctggttccgtctttgatttgggcggtgctgactccctgttgctgtttcttggccttggttgtggtgaatccag
||||| ||||| ||| |||||||| ||||||| || || || || ||||| ||||| ||  |||||||||||||||||||||||||||| || |||||||| |   |   |   | ||      ||      | ||  |||| |  |   |       |    ||   |||| || | |  | |       ||  || |    ||                     
ATCCGATTCATTCTGTTGCAGAACAGGCAGGGCAAGACCCGTCTTGCCAAATACTACGTTCCTCTCGAGGACTCCGAGAAGCACAAGGTCGAATACGAGGtaacaatttcgtcttccttcccacgatttc--acttcttcttcacacacaacagcaccttaacct--aattttggagata-taatgttggtttagtgatgaaagg---------------------

upper sequence: GRMZM2G052713_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA14G40430.1 (Glycine max), 5'ss of exon 2
ATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgctggac--tgctggtggagaaga--aagatttgatcttgatgccggattctggttccgtctttgatttgggcggtgctgactccctgttgctgtttcttggccttggttgtggtgaatccag
||||| ||||| ||| |||||||| ||||||| || || || || ||||| ||||| ||  |||||||||| ||||||||||||||||| || |||||||| |   | ||      |  |  |  | || |  |  |  | | | | ||    ||     | | |||||  |      | |  |  ||       | || |                             
ATCCGATTCATTCTGTTGCAGAACAGGCAGGGCAAGACCCGTCTTGCCAAATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAGgtaacaattctacttcttcttcatacacaacaccaccaccttaacctaattggagacataaggttcgtctacgggagaagagaaggggaagag--atcgcgg-----------------------------

upper sequence: GRMZM2G052713_T03 (Zea mays), 5'ss of exon 2
lower sequence: Vv18s0001g14240.t01 (Vitis vinifera), 5'ss of exon 3
ATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtg--agcctgctggactgctggtggagaagaaagatttgatcttgatgccggattctggttccgtctttgatttgggcggtgctgactccctgttgctgtttcttggccttggttgtggtgaatccag
||||| |||||  | || |||||| ||||||| || || || || ||||||||||||||  |||| || || ||||||||||||||||| || ||||||||   | |||  ||   | |   |       |  | |||  |  |      || || ||  |  ||  |||  |||                                                     
ATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAGTACTATGTTCCTCTTGAAGAATCCGAGAAGCACAAGGTCGAATACGAGgtattatcctcttgattttcctctctcttctacggttttctttcta-----gggttttgaat--gttattgtcttgtag--------------------------------------------------

upper sequence: GRMZM2G052713_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ11600 (Selaginella moellendorffii), 5'ss of exon 2
ATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcc--tgctggactgctggtggagaagaaagatttgatcttgatgccggattctggttccgtctttgatttgggcggtgctgactccctgttgctgtttcttggccttggttgtggtgaatccag
||  | ||||||||  |||| || || |||||||| || || || ||||||||||||||| | ||||| |||||||||||||| ||| |  |||| ||||| |  |  | |  || | |  |||  | ||    ||||     ||    || |                                                                           
ATTAGATTCATCCTCTTGCAAAATCGCCAGGGGAAGACTCGTCTCGCCAAGTACTATGTCCCGCTCGAAGACTCCGAGAAGCAAAAGCTCCAGTATGAGgtaaatcgctcccagatt-cgagtgttggagtggaattt----ctggcatcgcag--------------------------------------------------------------------------

upper sequence: GRMZM2G052713_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ09792 (Selaginella moellendorffii), 5'ss of exon 2
ATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcc--tgctggactgctggtggagaagaaagatttgatcttgatgccggattctggttccgtctttgatttgggcggtgctgactccctgttgctgtttcttggccttggttgtggtgaatccag
||  | ||||||||  |||| || || |||||||| || || || ||||||||||||||| | ||||| |||||||||||||| ||| |  |||| ||||| |  |  | |  || | |  |||  | ||    ||||  ||     || |                                                                             
ATTAGATTCATCCTCTTGCAAAATCGCCAGGGGAAGACTCGTCTCGCCAAGTACTATGTCCCGCTCGAAGACTCCGAGAAGCAAAAGCTCCAGTATGAGgtaaatcgctcccagatt-cgagtgttggagtggaatttc-tcgcatcgcag-----------------------------------------------------------------------------

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|60352004|gb|DN218977.1|DN218977
EST:     AGGTTGAGTACGAG                         GTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
genomic: AGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
EST: gi|211344140|gb|FL188310.1|FL188310
EST:     AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG                         GTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
genomic: AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
EST: gi|211344147|gb|FL188317.1|FL188317
EST:     AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG                         GTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACMAACTTCGTCGAG
genomic: AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
EST: gi|32938017|gb|CF042836.1|CF042836
EST:     AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG                         GTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
genomic: AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
EST: gi|211344138|gb|FL188308.1|FL188308
EST:     AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG                         GTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
genomic: AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
EST: gi|60394275|gb|DN227145.1|DN227145
EST:     GACTCCGAGAAGC-CAAGGTTGAGTACGAG                         GTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
genomic: GACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
EST: gi|67011386|gb|CO440135.1|CO440135
EST:     AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG                         GTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
genomic: AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
EST: gi|32936019|gb|CF040831.1|CF040831
EST:     AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG                         GTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
genomic: AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
EST: gi|211344136|gb|FL188306.1|FL188306
EST:     AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG                         GTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
genomic: AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
EST: gi|211344143|gb|FL188313.1|FL188313
EST:     AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG                         GTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
genomic: AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
EST: gi|211344148|gb|FL188318.1|FL188318
EST:     AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG                         GTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
genomic: AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
EST: gi|60351820|gb|DN218793.1|DN218793
EST:     GACTCCGAGAAGC-CAAGGTTGAGTACGAG                         GTGCATCNGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGA
genomic: GACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATC-GGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGA
EST: gi|211341751|gb|FL188301.1|FL188301
EST:     AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG                         GTGGNTCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
genomic: AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
EST: gi|211344139|gb|FL188309.1|FL188309
EST:     AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG                         GTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
genomic: AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
EST: gi|60356394|gb|DN223367.1|DN223367
EST:     AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG                         GTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
genomic: AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
EST: gi|211344141|gb|FL188311.1|FL188311
EST:     AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG                         GTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
genomic: AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
EST: gi|211341753|gb|FL188303.1|FL188303
EST:     AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG                         GTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
genomic: AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
EST: gi|211344137|gb|FL188307.1|FL188307
EST:     AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG                         GTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG
genomic: AGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG

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: 42 (upstream exon), 49 (downstream exon)
Score: 85

ATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

ATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG


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

ATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

ATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgc ... gtgaatccagGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgctggactgctggtggagaagaaagatttgatcttgatgccggattctggttccgtctttgatttgggcggtgctgactccctgttgctgtttcttggccttggttgtggtgaatccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC