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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCTGCTACGGCTGGGTGAGGCGGGGGGCTACTGCCGCCGCCTAACGCCAGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccctccttctgttcccttcccgctgtgtgaaaccgagcacccaaaccctatcatagagctatttgctagtatttgatgcctgccaacttccaac...

Basic information

species Zea mays
transcript GRMZM5G863152_T02
intron # 1
splice site 5'
intron type U2

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|211224001|gb|FL296369.1|FL296369
EST:     AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAG                         GGATGGTTGCNACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
genomic: AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
EST: gi|211223994|gb|FL296362.1|FL296362
EST:     AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAG                         GGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
genomic: AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
EST: gi|211226061|gb|FL296377.1|FL296377
EST:     AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAG                         GGATGGTTGCWACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
genomic: AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
EST: gi|211135925|gb|FL188995.1|FL188995
EST:     AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAG                         GGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAANATG
genomic: AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
EST: gi|211226060|gb|FL296376.1|FL296376
EST:     AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAG                         GGATGGTTGCRACAGATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGAT
genomic: AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACA-ATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGAT
EST: gi|71305070|gb|DR788672.1|DR788672
EST:     AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAG                         GGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
genomic: AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
EST: gi|211226055|gb|FL296371.1|FL296371
EST:     AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAG                         GGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
genomic: AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
EST: gi|211223996|gb|FL296364.1|FL296364
EST:     AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAG                         GGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
genomic: AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
EST: gi|211223997|gb|FL296365.1|FL296365
EST:     AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAG                         GGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
genomic: AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
EST: gi|76920373|gb|DV168136.1|DV168136
EST:     AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAG                         GGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
genomic: AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
EST: gi|211226059|gb|FL296375.1|FL296375
EST:     AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAG                         GGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCA-KGGTTCGAAGATG
genomic: AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
EST: gi|211226058|gb|FL296374.1|FL296374
EST:     AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAG                         GGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
genomic: AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
EST: gi|211224000|gb|FL296368.1|FL296368
EST:     AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAG                         GGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
genomic: AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
EST: gi|71432424|gb|DR813474.1|DR813474
EST:     AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAG                         GGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
genomic: AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
EST: gi|211223995|gb|FL296363.1|FL296363
EST:     AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAG                         GGATGGCTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
genomic: AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
EST: gi|211226057|gb|FL296373.1|FL296373
EST:     AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAG                         GGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
genomic: AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
EST: gi|78081578|gb|DV509990.1|DV509990
EST:     AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAG                         GGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
genomic: AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
EST: gi|211223993|gb|FL296361.1|FL296361
EST:     AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAG                         GGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG
genomic: AGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATG

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: 48 (upstream exon), 48 (downstream exon)
Score: 61

TCTCTGCTACGGCTGGGTGAGGCGGGGGGCTACTGCCGCCGCCTAACGCCAGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATGGTTCTCCATATGACCCACAATGTATTCAGTTTTCGATGCTTTGCTGCCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 72

TCTCTGCTACGGCTGGGTGAGGCGGGGGGCTACTGCCGCCGCCTAACGCCAGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATGGTTCTCCATATGACCCACAATGTATTCAGTTTTCGATGCTTTGCTGCCA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 16

TCTCTGCTACGGCTGGGTGAGGCGGGGGGCTACTGCCGCCGCCTAACGCCAGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATGGTTCTCCATATGACCCACAATGTATTCAGTTTTCGATGCTTTGCTGCCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 63

TCTCTGCTACGGCTGGGTGAGGCGGGGGGCTACTGCCGCCGCCTAACGCCAGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccct ... tatgttgtagGGATGGTTGCAACAATTTGGGCATAGCGTTGGTATCAGTGGTTCGAAGATGGTTCTCCATATGACCCACAATGTATTCAGTTTTCGATGCTTTGCTGCCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCTGCTACGGCTGGGTGAGGCGGGGGGCTACTGCCGCCGCCTAACGCCAGGTTCCGAGGCCTTCGTCGGTCTATTTGCCGGCGATGAACATCCACCAGgtaatcccctccttctgttcccttcccgctgtgtgaaaccgagcacccaaaccctatcatagagctatttgctagtatttgatgcctgccaacttccaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccttccc