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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGCTCTATGAAGACAACGAATATGCTCTCTACACTGTGACACTATTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagattttcttgagatttacgctttacattagtctggctatcctgctttagtcttttgtcgtccactaaattttttgtcatttgtttccag

Basic information

species Zea mays
transcript GRMZM2G144372_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144372_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 7
AAAGCTCTATGAAGACAACGAATATGCTCTCTACACTGTGACACTATTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagattt---tcttgagatttacgctttacattagtctggctatcctgctttagtcttttgtc------gtccactaaattttttgtcatttgtttccag------------------------------------------------------------------------------
||| || ||||| ||||| || |||||||||||||| || ||| | ||||||||||||||||||||||||||||||||||| || || || ||||| |||||||  ||    || | |  ||| |     | |    | |    |     | ||   ||||| ||      | |     | ||     | | |||   |                                                                                 
AAAACTTTATGAGGACAATGAGTATGCTCTCTACACGGTAACATTGTTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCACGTGAAAAAGGTTTCCAGgtaaatttgccgtcctaactttttcatcaaaaacctttgtttacacttcacatttagcttttatccctagagccttaggagttccaaataacttgggacagaaattcagtcttgtttttctgtccccatcaatctggcaattctctgtcacccattaacttgtattacgttgaaatacag
















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|60396077|gb|DN228946.1|DN228946
EST:     GCGAGAAGGGTTTTCAG                         ATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
genomic: GCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
EST: gi|116823457|gb|EC867003.1|EC867003
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         ATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
EST: gi|71428528|gb|DR809578.1|DR809578
EST:     TAAGGTTGTTGACAAACTTTA-GGTCCGTGCTCGCGAGAAGGGTTTTCAG                         ATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
genomic: TAAGGTTGTTGACAA-CTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
EST: gi|40336015|gb|CK370085.1|CK370085
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         ATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
EST: gi|76012957|gb|DT940127.1|DT940127
EST:     CGCGAGAAGGGTTTTCAG                         ATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
genomic: CGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
EST: gi|71428527|gb|DR809577.1|DR809577
EST:     CTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         ATCCGTGATTTGGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
genomic: CTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
EST: gi|61117885|gb|DN558846.1|DN558846
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         ATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
EST: gi|61117886|gb|DN558847.1|DN558847
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         ATCCGTGATTTCGAGTACAGTCCTGGAGCACAGGAAAGCCGGATGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
EST: gi|31558493|gb|CD527705.1|CD527705
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         ATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
EST: gi|61117883|gb|DN558844.1|DN558844
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         ATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
EST: gi|211430939|gb|FL367561.1|FL367561
EST:     ACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         ATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
genomic: ACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
EST: gi|67023340|gb|CO452089.1|CO452089
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         ATCCGTGATTTCGAGTACAGTCCTGAAGC-CAGGAAAGCCGGATGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
EST: gi|32910803|gb|CF015615.1|CF015615
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         ATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
EST: gi|71430058|gb|DR811108.1|DR811108
EST:     AAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         ATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
genomic: AAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
EST: gi|67010828|gb|CO439577.1|CO439577
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         ATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
EST: gi|31358589|gb|CD442946.1|CD442946
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         ATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
EST: gi|20811126|gb|BQ295604.1|BQ295604
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         ATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
EST: gi|67022208|gb|CO450957.1|CO450957
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         ATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
EST: gi|37390080|gb|CF632266.1|CF632266
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         ATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
EST: gi|61117882|gb|DN558843.1|DN558843
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         ATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAG

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: 46 (upstream exon), 49 (downstream exon)
Score: 182

AAAGCTCTATGAAGACAACGAATATGCTCTCTACACTGTGACACTATTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAGATGGAGAAGCTACTGCGAGACCAAGAAGCTATGAGGACCACTCTTCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

AAAGCTCTATGAAGACAACGAATATGCTCTCTACACTGTGACACTATTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAGATGGAGAAGCTACTGCGAGACCAAGAAGCTATGAGGACCACTCTTCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 139

AAAGCTCTATGAAGACAACGAATATGCTCTCTACACTGTGACACTATTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAGATGGAGAAGCTACTGCGAGACCAAGAAGCTATGAGGACCACTCTTCTTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 231

AAAGCTCTATGAAGACAACGAATATGCTCTCTACACTGTGACACTATTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaagatttt ... ttgtttccagATCCGTGATTTCGAGTACAGTCCTGAAGCACAGGAAAGCCGGATGCAGGAGATGGAGAAGCTACTGCGAGACCAAGAAGCTATGAGGACCACTCTTCTTC