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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttcgttacttatttcactttgccttggccttgctctgtggtgtattacgtgctatcttagcttaggtgacttgcgcatgttgatatcttggcc...

Basic information

species Zea mays
transcript GRMZM2G010823_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 16
AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttcgttacttatttcactttgccttggccttgctctgtggtgtattacgtgctatcttagctt--aggtgacttgcgcatgt-tgatatcttggcc--
||||||||||||||||||||||||||||||||||||||||| ||||||||||||| ||| ||||||||||| ||| | |||||| | || | ||| ||| ||| | | | || ||||| | |||||| || ||| | || || |
AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAGgtgattattc--catttattttagtt-gttttgattcgaaactgatgtgca--atggtctgcgttagccttaaggtgatatgtgcaaacataatttcatattttg

upper sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA10G02040.1 (Glycine max), 5'ss of exon 16
AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttcgttact-tatttcactttgccttggccttgctc--tgtggtgtattacgtgctatcttagcttaggtgacttgcg-catgttgatatcttggcc
|||||||| |||||||| || ||||| ||||| |||| |||||||||||| || || | |||||||| | | | | || || ||| | || | |||||| | || | || | ||| | | | | | | |||| || |
AAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAGgtgatgatgccatgttatacttgtttttccgtttgtcttgcttattttgacctctttctgaatattaaataaaaaatcatgtttgacatgcattaattct----

upper sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA02G01920.1 (Glycine max), 5'ss of exon 16
AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctt-tcgttacttatttcactttgccttggccttgctc--tgtggtgtattacgtgctatcttagcttaggtgacttgcgcatgttgatatcttggcc
|||||||| |||||||| || ||||| ||||| |||| |||||||||||| || || | |||||||| | || | || || ||| || | |||||| | || | || ||| | | || ||| || || ||||
AAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAGgtgatgatgtcatgttatacttgtttttctgtttgtcttgcttattttgacctctttttgaatattaaaaaaaaatcatgtttgacatattaat-tcttaa--

upper sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 16
lower sequence: AT5G50950.2 (Arabidopsis thaliana), 5'ss of exon 16
AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttcgttacttatttcactttgccttggccttgctctgtggtgtattacgtgctatcttagctt-aggtgacttgcgcatgtt------gatatcttggcc-------------------------------------------------------------------------------------------
|||||||||||||||||||||||||| || || || | ||| |||||||||||| ||| || ||||| | | | | |||| ||| | | || | | | ||| | | ||||| || || || |||||| |||| || |
AAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGgtaaaca---ataaactattaacgttttcatca--ctaaataaatcggaatttaaacccatttttagcaagagaaaacatgttcatgtttgttacaatatatttgttgttctattttggatttaaaccttctccagtgaaaattatataatacaatacctttgagatccctaaatctttgctttaatttattctatag

upper sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 16
lower sequence: AT2G47510.1 (Arabidopsis thaliana), 5'ss of exon 17
AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttcgttacttatt-tcactttgccttggccttgctctgtggt--gtattacgtgctatc-ttagcttaggtgacttgcgcatgttgatatcttggcc-----------------------------------------------------------------------
||||| || ||||||||||||||||| ||||| |||||||| |||||||||||| || |||||||| | | | || || | | | ||| ||| | | | | | ||| || | | ||| ||||||
AAAATCGGGTATGACAATGCTGCAGCAGTTGCCAAGAAAGCTCACAAAGAAGGATGTACATTGAAGgtaaacacaagaaacaatttattatagagaattgaaattgattggcaacaagagaaagacgttattgcctgcatcagcagtttgatagcaaatatatctgcaatgcagattacataaatttattgtaaacaggttctatagtatgttaaaccttgagttttaatttatcctacag

upper sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 16
lower sequence: Vv14s0060g01700.t01 (Vitis vinifera), 5'ss of exon 14
AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttcgttacttatttcactttgccttggcctt---gctctgtggtgtattacgtgctatcttagcttaggtgacttgcgcatgttgatatcttggcc
||||| |||||||| ||||||||||| ||||| |||||||| ||||| || |||||||| | |||||| |||| || ||| | | | || || | || |||| | | | || || | | | | || ||| |||
AAAATCGGCTATGATAATGCTGCAGCGGTTGCCAAGAAAGCTCACAAGGAGGGAACCACTCTTAAGgtggtcttattttccttcctatgcaataactgaaccctcgtgcattgtgttaggaaaattattaactcatttcacaatagtttgatgcattgcagatttg---

upper sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 16
lower sequence: PP1S49_154V6.1 (Physcomitrella patens), 5'ss of exon 16
AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttcgttacttatttcactttgccttg-gccttgctctgtggtgtattacgtgctatcttagcttaggtgacttgcgcatgttgatatcttggcc--
|||||||| |||||||| |||||||| ||| |||||||| ||||||||||| || || ||||||| | || | || | | || || || | | || ||| | | | | | | | | ||||| || || |
AAAATTGGTTATGACAAAGCTGCAGCATGTGCGAAGAAAGCTCACAAAGAAGGGACTACATTGAAGgcaagacctcagtttttgtgttgtgctgggttctgcagttaacaaaagtcatttatgcacgcttctgtttc---ttggatatggatgttaatgtcgcaccgcc

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|60342181|gb|DN209154.1|DN209154
EST:     ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG                         GAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
genomic: ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttc ... ttttccccagGAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
EST: gi|60357469|gb|DN224442.1|DN224442
EST:     ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG                         GAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
genomic: ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttc ... ttttccccagGAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
EST: gi|149081506|gb|EE170642.2|EE170642
EST:     ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG                         GAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
genomic: ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttc ... ttttccccagGAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
EST: gi|91868642|gb|EB400097.1|EB400097
EST:     ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG                         GAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
genomic: ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttc ... ttttccccagGAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
EST: gi|149089383|gb|EE178622.2|EE178622
EST:     ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG                         GAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
genomic: ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttc ... ttttccccagGAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
EST: gi|116829526|gb|EC868872.1|EC868872
EST:     ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG                         GAGGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCA
genomic: ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttc ... ttttccccagGAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCA
EST: gi|6022572|gb|AW067384.1|AW067384
EST:     ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG                         GAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
genomic: ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttc ... ttttccccagGAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
EST: gi|16926219|gb|BM079287.1|BM079287
EST:     ATGCTGCAACTGTTGATAAGAAAGCCCACAAAAAAGGAACCACGTTGAAG                         GAAACTGCATTAGACCTTGGAGTATTAACGGAGCAAAAATTCCATGAGCTT
genomic: ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttc ... ttttccccagGAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
EST: gi|5901092|gb|AW042192.1|AW042192
EST:     ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG                         GAAGCTGCATTAGACCTTGNAGTATTAACGGAGCAAGAATTCCATGAGCTT
genomic: ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttc ... ttttccccagGAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
EST: gi|78022604|gb|DV490991.1|DV490991
EST:     ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG                         GAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
genomic: ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttc ... ttttccccagGAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
EST: gi|6102108|gb|AW126578.1|AW126578
EST:     ATGCTGCAGCTGTTGTTAAGAAAGCCCNCAAAGAAGGANCCACGTTGAAG                         GAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
genomic: ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttc ... ttttccccagGAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
EST: gi|211208053|gb|FL436834.1|FL436834
EST:     ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG                         GAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
genomic: ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttc ... ttttccccagGAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTT
EST: gi|8930245|gb|BE225009.1|BE225009
EST:     ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG                         GAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGATATTTCATGAGCT
genomic: ATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttc ... ttttccccagGAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGA-ATTCCATGAGCT

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: 47 (upstream exon), 49 (downstream exon)
Score: 282

AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttc ... ttttccccagGAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTTGTCGTCCCGGAGAAAATGATTGGTCCTTCTGATTGATAACCCCATGTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 457

AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttc ... ttttccccagGAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTTGTCGTCCCGGAGAAAATGATTGGTCCTTCTGATTGATAACCCCATGTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 492

AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttc ... ttttccccagGAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTTGTCGTCCCGGAGAAAATGATTGGTCCTTCTGATTGATAACCCCATGTTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 452

AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttc ... ttttccccagGAAGCTGCATTAGACCTTGGAGTATTAACGGAGCAAGAATTCCATGAGCTTGTCGTCCCGGAGAAAATGATTGGTCCTTCTGATTGATAACCCCATGTTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttcgttacttatttcactttgccttggccttgctctgtggtgtattacgtgctatcttagcttaggtgacttgcgcatgttgatatcttggcc

- - - - - - - - ATGCTG
- - - - - - - - TGCTGC
- - - - - - - - - CTGCAG
- - - - - - - - - - GCAGCT
- - - - - - - - - - - CAGCTG
- - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG