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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgttttcagttaaccgctttgtacgaaaacaagcattaatcctatcttgatttcctttttaacttgtaatttatgttttttggtcaattgtcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA

Basic information

species Zea mays
transcript GRMZM2G113470_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113470_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g08660.1 (Oryza sativa), 3'ss of exon 2
--cgttttcagttaaccgctttgtacgaaaacaagcattaatcctatcttgatttcctttttaacttgtaatttatgttttttggtcaattgtcatga----atagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA
   | | | |  |  ||||| |   |    |   ||  |  |  |  ||    |||||| ||  || |||| | || ||  ||    | |    |  |    | |||| ||||||||||||||||| |||||| | |||||||||||||||||  | || || |||||||||||||| ||| |||| ||  | |||||||  ||| 
tctgatgttaagttgccgctcttctc----atttgccct--ttttggctactgttccttgttttctggtaactaatcttggttaaatattatctacaattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTCTACGTCTACTGGATATGCCCTTTTGTTGGCGCTGTTCTTGCTGCCTGGG

upper sequence: GRMZM2G113470_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G26720.1 (Glycine max), 3'ss of exon 2
cgttttcagttaaccgctttgtacgaaaacaagcattaatcctatcttgatttccttttta-acttgtaatttatgttttttggtcaattgtcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA
  |   || ||      ||||  |   ||||     || |  | |  || | |   |  || |    | ||  ||   |    |     | | ||    |||||||||| ||||||||  || | || ||||||||||||||||| ||  | ||||| |||||||| ||||||||  |||| || || || |||| |||| 
-ctgaccattttttgtttttggtcagtaacataagatattaatgtaatgttgtgagtcatatatgcatgatgaataactcaatgattggtattattttcagGCATTTGGTTGGGCATACTTTGAAAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGCCCCTTCTTTGGAGCAATACTGGCTGCATGGC

upper sequence: GRMZM2G113470_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA19G28430.1 (Glycine max), 3'ss of exon 2
cgttttcagttaaccgctttgtacgaaaacaagcattaatcctatcttgatttcctttttaacttgtaatttatgtt------ttttggtcaattgtcatgaat--agGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA
         ||  |   ||| |       |     |||||   |  ||||||   || |  || |  |  |     |       | || ||  || |  |   |  |||| ||||||||||||||  | ||||| ||||||||||||||||| ||  | ||||| |||||||| || ||||| |  || || ||  | ||||  ||| 
--------cttctcttgtttttgaatcttctgattttaatttcagtttgattaggttctagacctagagatgccaatgaataactgtgatcggttattgtccctgcagGCTTTTGGCTGGGCATACTTAAACAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGTCCCTTCACCGGAGCAATATTGGCTGCTTGGC

upper sequence: GRMZM2G113470_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G04800.1 (Glycine max), 3'ss of exon 2
---cgttttcagttaaccgctttgtacgaaaacaagcattaatcctatcttgatttcct--ttttaacttgtaatttatgttttttggtcaattgtcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA
   | | ||   | || |   |  |   || |  ||  | | |    ||| || ||     ||  ||    ||| || |||  | || |  ||||||      |||| ||||||||||||||  | ||||| ||||||||||||||||| ||  | ||||| |||||||| ||||||||    || || ||  | ||||  ||| 
tctcatgtttt-tgaatcttctgatgttaatatcagtttgattagggtctagacttagagattccaatgaataactt-tgtgatgtgtt--attgtc-cctgcagGCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGCCCCTTCGCCGGAGCAATATTGGCTGCTTGGC

upper sequence: GRMZM2G113470_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G07680.1 (Glycine max), 3'ss of exon 2
cgttttca--gttaaccgctttgtacgaaaacaagcattaatcctatcttgatttcctttttaacttgtaatttatgttttttggtcaattgtcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA
| || | |   ||     |||| |   | |  |    |||||   || |||     | | |  |    ||||  ||   |    |     | | ||    |||||||||| ||||||||  || | || ||||||||||||||||| ||  | ||||| |||||||| ||||||||  |||| || || || |||| |||| 
ctttctgaccatttttttctttttgtaacataagatgttaatgtaatgttgtgagtcatat--atgcataatgaataactcaatgattggtattattttcagGCATTTGGTTGGGCATACTTTGAAAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGCCCCTTCTTTGGAGCAATACTAGCTGCATGGC

upper sequence: GRMZM2G113470_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv08s0007g07680.t01 (Vitis vinifera), 3'ss of exon 2
cgttttcagttaaccgctttgtacgaaaacaagcattaatcctatcttgatttcctt-tttaacttgtaatttatgttttttggtcaattgtcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA
 |||      | ||   ||   | ||     ||||||       ||    || | || |||||      | |||| ||| |   |   ||||| |    |||||||||| ||||||||| | ||||||||||| ||||||||||| ||| |||| || |||||||| |||||||| || ||||| ||  | |||| |||| 
tgttggggcattacgatttgaaatgatggtcagcatttccttgctcccttttccattatttaaaagcctaattatatttatatttattttgtc-tctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTGTACGTTTACTGGATCTGCCCCTTCATAGGGGCAATATTGGCTGCATGGG

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|32796742|gb|CD948978.1|CD948978
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCGTATGTTA
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTA
EST: gi|211350454|gb|FL030225.1|FL030225
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|32787717|gb|CD936619.1|CD936619
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTA
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTA
EST: gi|9961456|gb|BE644439.1|BE644439
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|32789470|gb|CD941706.1|CD941706
EST:     TCATCCTCGCAGGCGCAGAGTACACGGNGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGC
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGC
EST: gi|32799406|gb|CD951642.1|CD951642
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGC
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGC
EST: gi|15208907|gb|BI430791.1|BI430791
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|211350458|gb|FL030229.1|FL030229
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|8576937|gb|BE129574.1|BE129574
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCGTATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|32796050|gb|CD948286.1|CD948286
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCGTATGTTA
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTA
EST: gi|32806579|gb|CD958813.1|CD958813
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCAGGGCGTATGTTA
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTA
EST: gi|4827620|gb|AI668312.1|AI668312
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|211350457|gb|FL030228.1|FL030228
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCGTATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|78025445|gb|DV493832.1|DV493832
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|149100062|gb|EE186113.2|EE186113
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|211350456|gb|FL030227.1|FL030227
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCGTATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|32797913|gb|CD950149.1|CD950149
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGC
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGC
EST: gi|149100063|gb|EE186114.2|EE186114
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|32801538|gb|CD953774.1|CD953774
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGC
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGC
EST: gi|32789714|gb|CD941950.1|CD941950
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTA
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTA
EST: gi|60353657|gb|DN220630.1|DN220630
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGATAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|78179554|gb|DV549927.1|DV549927
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCGTATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|211350455|gb|FL030226.1|FL030226
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|14701476|gb|BI233894.1|BI233894
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG

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: 28

CCGCAACGTCATCCTCAAGACCTTGCTGCTCTCAACCTCCATCGTCTCCGTCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 53

CCGCAACGTCATCCTCAAGACCTTGCTGCTCTCAACCTCCATCGTCTCCGTCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 58

CCGCAACGTCATCCTCAAGACCTTGCTGCTCTCAACCTCCATCGTCTCCGTCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 36

CCGCAACGTCATCCTCAAGACCTTGCTGCTCTCAACCTCCATCGTCTCCGTCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgatttcctttttaacttgtaatttatgttttttggtcaattgtcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA
           ttttaac  putative branch site (score: 36)
          tttttaacttgtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgttttcagttaaccgctttgtacgaaaacaagcattaatcctatcttgatttcctttttaacttgtaatttatgttttttggtcaattgtcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - -aaaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttt