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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAATGGGAACAAGCGGGTCACTTGATGGGCAGCAAAGGTTGGTGATCAAAGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatccaatttgatcgcgttgatacttgtagtatgcttttttttttttgaacagatgatgttataagctacttgctgtttgctgatatgattgaataaatatgatggttgtttattgtttttctccctgctatctgaaagttgactcatttctcag

Basic information

species Zea mays
transcript GRMZM2G080048_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080048_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g48300.1 (Oryza sativa), 5'ss of exon 8
GAAATGGGAACAAGCGGGTCACTTGATGGGCAGCAAAGGTTGGTGATCAAAGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatccaatttgatcgcgttgatacttgtagtatgcttttttttttttgaaca-gatga--tgttataagcta----cttgctgtttgctgatatgattgaataaatatgatggttgtttattgtttttctccctgctatctgaaagttgactcatttctcag
|||||||| ||||| || |||||||||||||||||||||||||||||||||||||||||||| || |||||||| |||||||||||| ||||||| ||||||||||||||| | || ||  | ||| |        |  ||||    |||||       | | |  | | ||||| |      ||| ||||| ||| | || | |  | | |    |     |||   |  ||     |  ||   ||    || |   |  | ||||
GAAATGGGGACAAGTGGATCACTTGATGGGCAGCAAAGGTTGGTGATCAAAGGAAGATTTGCTCCGAAAAACTTCGAAGCAATCCTGCGGAGATATATCAgtaagttatcctacttcattcccttggttgaacagatgagcttcccctttttcatgtgtggtaaactatcataagttgtacgtttgttgtttactgttttgttagtgttagttgacttaagatttcaagggttatatgcaacttattgcgtctttaa--acctttcag
















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|71300898|gb|DR786478.1|DR786478
EST:     AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|60399446|gb|DN232258.1|DN232258
EST:     AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|4646971|gb|AI622046.1|AI622046
EST:     GGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAAGATACATCA                         ATGAGTACGTCATCTGCA
genomic: GGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGA-GATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCA
EST: gi|37383473|gb|CF628753.1|CF628753
EST:     AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|211375010|gb|FL430791.1|FL430791
EST:     AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|60354326|gb|DN221299.1|DN221299
EST:     AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|6527068|gb|AW216283.1|AW216283
EST:     AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|94473773|gb|EB702731.1|EB702731
EST:     AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|32863955|gb|CF003637.1|CF003637
EST:     AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|26455990|gb|CA827573.1|CA827573
EST:     AGGAAGATTTGCCCCCAAAAATTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|211252876|gb|FL444298.1|FL444298
EST:     GGGAAGATTTGCCCCCAAAAACTTCGAAGCAATCGTGAGGAGATACATCA                         ATGAGTATGTCATCTGCAATGGATGCAAGAGCCCTGATTCCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|6031557|gb|AW076459.1|AW076459
EST:     AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|60357822|gb|DN224795.1|DN224795
EST:     AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|19822348|gb|BQ048372.1|BQ048372
EST:     AGGAAGATTTGCCCCCAAAAATTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|211028365|gb|FL441143.1|FL441143
EST:     AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|60395435|gb|DN228305.1|DN228305
EST:     AGGAAGATTTGCCCCCAAAAATTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|32863956|gb|CF003638.1|CF003638
EST:     AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|14191391|gb|BG833621.1|BG833621
EST:     AGGAAGATTTGCCCCCAAAAATTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATGACCATTCTGTCC
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGAT-ACCATTCTGTCC
EST: gi|211047495|gb|FL474402.1|FL474402
EST:     AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|60396947|gb|DN229766.1|DN229766
EST:     AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|60347700|gb|DN214673.1|DN214673
EST:     AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|27521993|gb|CA989099.1|CA989099
EST:     AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|60398984|gb|DN231800.1|DN231800
EST:     AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: AGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
EST: gi|60349100|gb|DN216073.1|DN216073
EST:     GGAAGATTTGCCCCCAAAAACTTTGAAGCAATCGCTGGGGAGATACATCA                         ATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA
genomic: GGAAGATTTGCCCCCAAAAACTTTGAAGCAATC-CTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCA

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), 48 (downstream exon)
Score: 206

GAAATGGGAACAAGCGGGTCACTTGATGGGCAGCAAAGGTTGGTGATCAAAGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 187

GAAATGGGAACAAGCGGGTCACTTGATGGGCAGCAAAGGTTGGTGATCAAAGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 122

GAAATGGGAACAAGCGGGTCACTTGATGGGCAGCAAAGGTTGGTGATCAAAGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 240

GAAATGGGAACAAGCGGGTCACTTGATGGGCAGCAAAGGTTGGTGATCAAAGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatc ... catttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAATGGGAACAAGCGGGTCACTTGATGGGCAGCAAAGGTTGGTGATCAAAGGAAGATTTGCCCCCAAAAACTTTGAAGCAATCCTGAGGAGATACATCAgtaagttatccaatttgatcgcgttgatacttgtagtatgcttttttttttttgaacagatgatgttataagctacttgctgtttgctgatatgattgaataaatatgatggttgtttattgtttttctccctgctatctgaaagttgactcatttctcag

- - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT