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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtcctatggctttgttgtttgttctcatgccttttgcagctttggctacttacaatgtacttatatcttctttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGATGCAAACATGGCCGAAGCTTCAGATGGAGCCGAGAAGATGGACACAGATG

Basic information

species Zea mays
transcript GRMZM2G021742_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G021742_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g13990.3 (Oryza sativa), 3'ss of exon 6
gtaatgtcctatggctttgttgtttgttctcatgccttttgcagctttggcta-cttacaatgtacttatatcttcttt-----------gtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGATGCAAACATGGCCGAAGCTTCAGATGGAGCCGAGAAGATGGACACAGATG
     ||   ||| | ||    || | ||    || || | ||| || |   | || || |||  || | || |  |||            || | ||| ||| |||||||||||| ||||||||||||||||| | |||| ||| ||||| || ||||| || |||||||| | | | || |||||||| |||||||
-----gtagcatgtcctttcgtttagctcctgcgctttgtacagtttggaacagctaactatgggctcacatttctttttcactactgtgatgattagGCACTGAGCACTGGCCAAATTCCTGCTGAATTTGCAATCCCCAAGCCAGATGCTAATATGGCTGATGCTTCAGAGGAAACTGAAAAGATGGAGACAGATG
















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|148969289|gb|EE020059.2|EE020059
EST:     CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG                         GTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
genomic: CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAGgtaatgtcct ... ttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
EST: gi|50326107|gb|CO521233.1|CO521233
EST:     CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG                         GTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
genomic: CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAGgtaatgtcct ... ttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
EST: gi|78117951|gb|DV536338.1|DV536338
EST:     CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG                         GTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
genomic: CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAGgtaatgtcct ... ttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
EST: gi|71446950|gb|DR828000.1|DR828000
EST:     CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG                         GTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
genomic: CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAGgtaatgtcct ... ttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
EST: gi|71317917|gb|DR795718.1|DR795718
EST:     CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG                         GTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
genomic: CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAGgtaatgtcct ... ttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
EST: gi|60356065|gb|DN223038.1|DN223038
EST:     CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG                         GTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
genomic: CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAGgtaatgtcct ... ttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
EST: gi|78118268|gb|DV536655.1|DV536655
EST:     CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG                         GTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
genomic: CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAGgtaatgtcct ... ttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
EST: gi|211124519|gb|FL463077.1|FL463077
EST:     CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG                         GTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAAGCCCGAT
genomic: CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAGgtaatgtcct ... ttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
EST: gi|31364112|gb|CD448467.1|CD448467
EST:     CTGCTATTGCAAATGCCCACACTCTTGAGGAAGCTGCAAGGCTAGAACAG                         GTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCGAAGCCCGAT
genomic: CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAGgtaatgtcct ... ttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
EST: gi|91053554|gb|EB163972.1|EB163972
EST:     CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG                         GTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
genomic: CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAGgtaatgtcct ... ttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
EST: gi|211242314|gb|FL469535.1|FL469535
EST:     CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG                         GTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
genomic: CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAGgtaatgtcct ... ttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
EST: gi|60356070|gb|DN223043.1|DN223043
EST:     CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG                         GTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
genomic: CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAGgtaatgtcct ... ttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT
EST: gi|5650116|gb|AI920476.1|AI920476
EST:     CTGCTATTGCAAATGCCCACACTCTTGAGGAAGCTGCAAGGCTAGAACAG                         GTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAAGCCCGAT
genomic: CTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAGgtaatgtcct ... ttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGAT

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), 49 (downstream exon)
Score: 288

GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAGgtaatgtcct ... ttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGATGCAAACATGGCCGAAGCTTCAGATGGAGCCGAGAAGATGGACACAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAGgtaatgtcct ... ttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGATGCAAACATGGCCGAAGCTTCAGATGGAGCCGAGAAGATGGACACAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 170

GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAGgtaatgtcct ... ttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGATGCAAACATGGCCGAAGCTTCAGATGGAGCCGAGAAGATGGACACAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAGgtaatgtcct ... ttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGATGCAAACATGGCCGAAGCTTCAGATGGAGCCGAGAAGATGGACACAGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgccttttgcagctttggctacttacaatgtacttatatcttctttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGATGCAAACATGGCCGAAGCTTCAGATGGAGCCGAGAAGATGGACACAGATG
                    tacttac  putative branch site (score: 118)
                                 cttatatcttcttt  putative PPT
                               tacttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtcctatggctttgttgtttgttctcatgccttttgcagctttggctacttacaatgtacttatatcttctttgtgctcagGTACTAAGCACTGGCCAAGTTCCTGCTGAATTTGCAGTGCCCAGGCCCGATGCAAACATGGCCGAAGCTTCAGATGGAGCCGAGAAGATGGACACAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG