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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCCTCACCAGTGCTGCCCCGAAAATGAAACCGGGTTTCGACCCTAGCAAAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgatgagtcttgtccaagcttgtatgccaattagtcgaatttgttattggacagtttagtttgtgataacattggttgtggttgtttag

Basic information

species Zea mays
transcript GRMZM2G068244_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068244_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g60740.1 (Oryza sativa), 5'ss of exon 2
AATCCTCACCAGTGCTGCCCCGAAAATGAAACCGGGTTTCGACCCTAGCAAAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgatgagtcttgtccaagcttgtatgccaattagtcgaatttgttattggacagtttagtttgtgataacattggttgtggttgtttag
||||||||| |||||||  || || |||||||| ||||| |||||||||||||||||  |||| ||||| ||||| ||||| |||||||| ||||| ||||| || ||||          | || |  |||         | |||| || |  |  ||   | || |  || ||| | | | ||||||   ||||
AATCCTCACGAGTGCTGTGCCAAAGATGAAACCTGGTTTTGACCCTAGCAAAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAGgttggctgattgaaacccctctagttaatata--------tagaatgtgattgtaaacttctgagctcatgctaatacttgctgtggtctgttag
















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|211286491|gb|FL310015.1|FL310015
EST:     AAGGYGGACGGCCCGAGTTCTACTACGAAGACGGAATGTWCCCTGAACAG                         GTGGAYTGGGTTGGCCCAAAGAATCAGATCGATGCTGC
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTGC
EST: gi|60397802|gb|DN230618.1|DN230618
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|20803051|gb|BQ294101.1|BQ294101
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|211277743|gb|FL328157.1|FL328157
EST:     AAGGTGCACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|211115046|gb|FL357306.1|FL357306
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|211096669|gb|FL353593.1|FL353593
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGT
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGT
EST: gi|116828080|gb|EC872039.1|EC872039
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|211196275|gb|FL364467.1|FL364467
EST:     AAGGTGCACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTGCTAAAGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTGCTAAAGCTG
EST: gi|211122932|gb|FL351238.1|FL351238
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|211098075|gb|FL308898.1|FL308898
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCC
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCC
EST: gi|211476034|gb|FL363764.1|FL363764
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCC
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCC
EST: gi|60339573|gb|DN206546.1|DN206546
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|211283841|gb|FL366659.1|FL366659
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|211537318|gb|FL320573.1|FL320573
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|211297500|gb|FL325965.1|FL325965
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACC-TGAACAG                         GTGGATTGGGTTGGCCAA
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAA
EST: gi|211517611|gb|FL357265.1|FL357265
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACRGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCCAAAGAATCAGATCGATGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|211100738|gb|FL316242.1|FL316242
EST:     AGGTGGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAHTCAGATCGATGCTG
genomic: AGGTGG-ACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|60343124|gb|DN210097.1|DN210097
EST:     TACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: TACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|211277770|gb|FL330868.1|FL330868
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|211077629|gb|FL313497.1|FL313497
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|211047467|gb|FL364281.1|FL364281
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|32911901|gb|CF016713.1|CF016713
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|211205798|gb|FL341896.1|FL341896
EST:     AAGGTGCACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTGC
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTGC
EST: gi|13125919|gb|BG316594.1|BG316594
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGG
EST: gi|32844239|gb|CD983920.1|CD983920
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|211383905|gb|FL356604.1|FL356604
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAA-CAGATCGATGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|211404942|gb|FL354737.1|FL354737
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTWCCCTGAACAG                         GTGGATTGGGTTGG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGG
EST: gi|60396304|gb|DN229173.1|DN229173
EST:     AATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: AATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|211132284|gb|FL314479.1|FL314479
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|211088423|gb|FL316647.1|FL316647
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTGCTAA
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTGCTAA
EST: gi|211069778|gb|FL326749.1|FL326749
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAAGAATCAGATCGATGCTGCTAAAGCT
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAA-GAATCAGATCGATGCTGCTAAAGCT
EST: gi|32920219|gb|CF025031.1|CF025031
EST:     ACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: ACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|13198686|gb|BG354488.1|BG354488
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
EST: gi|211414922|gb|FL346514.1|FL346514
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCG
EST: gi|211105758|gb|FL317208.1|FL317208
EST:     AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAG                         GTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG
genomic: AAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG

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: 198

AATCCTCACCAGTGCTGCCCCGAAAATGAAACCGGGTTTCGACCCTAGCAAAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 461

AATCCTCACCAGTGCTGCCCCGAAAATGAAACCGGGTTTCGACCCTAGCAAAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

AATCCTCACCAGTGCTGCCCCGAAAATGAAACCGGGTTTCGACCCTAGCAAAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 215

AATCCTCACCAGTGCTGCCCCGAAAATGAAACCGGGTTTCGACCCTAGCAAAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgat ... ggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCCTCACCAGTGCTGCCCCGAAAATGAAACCGGGTTTCGACCCTAGCAAAGGTGGACGGCCCGAGTTCTACTACGAAGACGGAATGTACCCTGAACAGgtgggttgatgagtcttgtccaagcttgtatgccaattagtcgaatttgttattggacagtttagtttgtgataacattggttgtggttgtttag

- - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA