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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCTTGCTGGGAGTAAAAGGTTGGCATTGTTTCTTGACTATGACGGAACACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAGgtatgttttccctaagtccttttaaaattagcagtccagtgcaatttcagttcgctttctaaacattgtattcacag

Basic information

species Zea mays
transcript GRMZM2G178546_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178546_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g40555.1 (Oryza sativa), 5'ss of exon 2
TGATCTTGCTGGGAGTAAAAGGTTGGCATTGTTTCTTGACTATGACGGAACACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAGgtatgttttc------cctaagtccttttaaaattagcagt-ccagtgcaatttcagttcgc---tttctaaacattgtattc-acag
| |||||||  |  ||||||| |||||| |||| ||||| ||||| ||||| ||||||||||||||||||||||||||||||||| |||||||||| |||||||  |||       | || || ||||     | |  | |  ||||| || || |  | ||   ||| |||| ||| ||||| ||||
TAATCTTGCCAGAGGTAAAAGATTGGCACTGTTCCTTGATTATGATGGAACTCTTTCACCGATTGTGGACAATCCTGAAAATGCAGTAATGTCTGACGAGgtattctttttctcctcttatgttctttagtcctcattattatcagtgaaaatttatctggcagttttgtaaatattctattcgacag

upper sequence: GRMZM2G178546_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA04G13880.1 (Glycine max), 5'ss of exon 3
TGATCTTGCTGGGAGTAAAAGGTTGGCATTGTTTCTTGACTATGACGGAACACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAGgtatgt-----tttccctaagtcc--ttttaaaattagcagtccagtgcaatttcagttcgctttctaaacattgtattcacag----------------
  |   |||     | || ||  | ||||||||||| || ||||| || || |||||||| |||||||| ||||||||   ||| || ||||| ||  | ||||||     | ||  |   |    | |  | |||  ||||    ||   ||||   ||   || |     |  |  ||  |                 
CAACTGTGCAAAAGGGAAGAGAATAGCATTGTTTCTGGATTATGATGGGACTCTTTCACCCATTGTGGATAATCCTGACTCTGCTTTCATGTCAGACAATgtatgtaatgctctcttttgatttagtgtccagattttcagttagatgtt-tttcttctcatgttgttgctttgctgatctgaccctgaaacttctgcag

upper sequence: GRMZM2G178546_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA06G47630.2 (Glycine max), 5'ss of exon 2
TGATCTTGCTGGGAGTAAAAGGTTGGCATTGTTTCTTGACTATGACGGAACACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAGgtatgt-----tttccctaagtcc--ttttaaaattagcagtccagtgcaatttcagttcgctttctaaacattgtattcacag----------------
  |   |||     | || ||  | ||||||||||| || ||||| ||||| |||||||| |||||||||||||||||   ||| || ||||| ||  | ||||||     | ||  |   |    | |  | |||  || |   |||   ||||   ||   || | | | |  |  ||  |                 
CAACTGTGCAAAAGGAAAGAGAATAGCATTGTTTCTGGATTATGATGGAACTCTTTCACCCATTGTGGACAATCCTGACTGTGCTTTCATGTCAGACAATgtatgtaatgctgtcttttgatttagtgtccagattttcaattaggtgtt-tttcttctcttgttattaccttgatgatctgatcctgaaacttctgcag

upper sequence: GRMZM2G178546_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G36570.1 (Glycine max), 5'ss of exon 3
TGATCTTGCTGGGAGTAAAAGGTTGGCATTGTTTCTTGACTATGACGGAACACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAGgtatgt-----tttccctaagtccttttaaaattagcagtccagtgcaatttcagttcgctttc--taaacattg--tattcacag-----------------
  |   |||     | |||||  | || |||||| | || ||||| ||||| ||||||||||||||||| ||||||||   ||| || ||||| ||  | ||||||     | ||| |  ||    |    || |  |   || |    ||| | |    | ||  |   | |||  || | |||                  
AAACTATGCAAAAGGGAAAAGAATTGCGTTGTTTATGGATTATGATGGAACTCTTTCACCGATTGTGGATAATCCTGACTGTGCTTTCATGTCCGACAATgtatgtggtactctccttgggtttactatccataataacatcaattgggttttattctattctcatttttctttggctaattacaattctgttaactctgcag

upper sequence: GRMZM2G178546_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G51460.2 (Arabidopsis thaliana), 5'ss of exon 2
TGATCTTGCTGGGAGTAAAAGGTTGGCATTGTTTCTTGACTATGACGGAACACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAGgtatgttttcc-ctaagtccttttaaaattagcagtc----cagtgcaatttca--gttcgctttctaaac--attgtat---tcacag----------------
   | ||||     | |||||  | |||||||||||||| |||||||| |||||||| || ||||| ||  | |||||   |||||  |||||   ||  ||| |||||   ||     || ||||| | |   |      |||  ||| ||     |||    ||  ||   ||| |||   ||||                  
GAGTTTTGCAAAAGGCAAAAGAATAGCATTGTTTCTTGATTATGACGGGACACTTTCGCCTATTGTTGAGGAACCTGATTGTGCATACATGTCAAGTGCTgtaagtttttaactttcctctattaaattcaattgctaaaacagatcaaatttgtgattcatcctcataatgaattatatggttcacgcctttttacatgtttag

upper sequence: GRMZM2G178546_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S32_182V6.1 (Physcomitrella patens), 5'ss of exon 3
TGATCTTGCTGGGAGTAAAAGGTTGGCATTGTTTCTTGACTATGACGGAACACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAGgtatgttt-tccctaagtccttt---------taaaattagcagt-ccagtgcaatttcagtt--------cgctttctaaacatt-gtattcacag---
  | |   |    |  ||     | |   | || ||||| |||||||||||||||||||| ||||||||  ||||||||   || || ||||| |  |||||  ||   |   |||||  |||         |  ||   | ||| |    |    ||||||          ||||| ||||  ||  ||||||      
CAAGCAGTCGCACAACAAGCAAATCGTGGTATTCCTTGATTATGACGGAACACTTTCACCCATTGTGGAGGATCCTGAACGGGCTTTCATGTCAGCCGAGgtcagtacatttttaagtattttgttaagcgatggaaagggtagtactgacggccattcagtgatacccggtgctttttaaatgttcatattcagtaaat

upper sequence: GRMZM2G178546_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S333_42V6.1 (Physcomitrella patens), 5'ss of exon 2
TGATCTTGCTGGGAGTAAAAGGTTGGCATTGTTTCTTGACTATGACGGAACACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAGgtatgttttccctaagtccttttaaaattagcagtc--cagtgcaatttcagttcgctttctaaacat---tgtattcacag------------------------------------------------------------
| | | ||| |  |  ||     | |   | |||||||||||||| |||||||||||||| ||||||||  |||| ||    || || ||||| |  |||||  ||    | |      ||||  ||| || ||    || | | |     | ||       ||| ||   ||  ||| ||                                                             
TAAGCATGCGGTTAAAAAGCAAATTGTGGTATTTCTTGACTATGATGGAACACTTTCACCCATTGTGGAGGATCCGGAGCGGGCCTTTATGTCAGCCGAGgtcagtacgtcttgtagtgttttggaatgagaaggaaacatttccacgctcgatcagcactgaaagatagatgatttctcaatgaggtcaaccgtgtagccggtactaaaagtacttttttattttattttatgctcaacag

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|31350805|gb|CD435162.1|CD435162
EST:     CACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAG                         ATGCGTGCTGCAGTGAGGCATGCGGCATCACTTTTCCCAACTGCAATCATT
genomic: CACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAGgtatgttttc ... gtattcacagATGCGTGCTGCAGTGAGGCATGCGGCATCACTTTTCCCAACTGCAATCATT
EST: gi|31349982|gb|CD434339.1|CD434339
EST:     CACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAG                         ATGCGTGCTGCAGTGAGGCATGCGGCATCACTTTTCCCAACTGCAATCATT
genomic: CACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAGgtatgttttc ... gtattcacagATGCGTGCTGCAGTGAGGCATGCGGCATCACTTTTCCCAACTGCAATCATT
EST: gi|19350662|gb|BM895194.1|BM895194
EST:     CACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAG                         ATGCGTGCTGCAGTGAGGCATGCGGCATCACTTTTCCCAACTGCA-TCATT
genomic: CACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAGgtatgttttc ... gtattcacagATGCGTGCTGCAGTGAGGCATGCGGCATCACTTTTCCCAACTGCAATCATT
EST: gi|19351740|gb|BM896272.1|BM896272
EST:     CACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAG                         ATGCGTGCTGCAGTGAGGCATGCGGCATCACTTTTCCCAACTGCAATCATT
genomic: CACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAGgtatgttttc ... gtattcacagATGCGTGCTGCAGTGAGGCATGCGGCATCACTTTTCCCAACTGCAATCATT
EST: gi|22491306|gb|BU051229.1|BU051229
EST:     CACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAG                         ATGCGTGCTGCAGTGAGGCATGCGGCATCACTTTTCCCAACTGCAATCATT
genomic: CACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAGgtatgttttc ... gtattcacagATGCGTGCTGCAGTGAGGCATGCGGCATCACTTTTCCCAACTGCAATCATT
EST: gi|149101959|gb|EE287477.2|EE287477
EST:     CACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAG                         ATGCGTGCTGCAGTGAGGCATGCGGCATCACTTTTCCCAACTGCAATCATT
genomic: CACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAGgtatgttttc ... gtattcacagATGCGTGCTGCAGTGAGGCATGCGGCATCACTTTTCCCAACTGCAATCATT
EST: gi|148937901|gb|EC882124.2|EC882124
EST:     CACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAG                         ATGCGTGCTGCAGTGAGGCATGCGGCATCACTTTTCCCAACTGCA
genomic: CACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAGgtatgttttc ... gtattcacagATGCGTGCTGCAGTGAGGCATGCGGCATCACTTTTCCCAACTGCA

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), 46 (downstream exon)
Score: 71

TGATCTTGCTGGGAGTAAAAGGTTGGCATTGTTTCTTGACTATGACGGAACACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAGgtatgttttc ... gtattcacagATGCGTGCTGCAGTGAGGCATGCGGCATCACTTTTCCCAACTGCAATCATTAGCGGAAGATCTCGTGATAAG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 23

TGATCTTGCTGGGAGTAAAAGGTTGGCATTGTTTCTTGACTATGACGGAACACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAGgtatgttttc ... gtattcacagATGCGTGCTGCAGTGAGGCATGCGGCATCACTTTTCCCAACTGCAATCATTAGCGGAAGATCTCGTGATAAG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 28

TGATCTTGCTGGGAGTAAAAGGTTGGCATTGTTTCTTGACTATGACGGAACACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAGgtatgttttc ... gtattcacagATGCGTGCTGCAGTGAGGCATGCGGCATCACTTTTCCCAACTGCAATCATTAGCGGAAGATCTCGTGATAAG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 49

TGATCTTGCTGGGAGTAAAAGGTTGGCATTGTTTCTTGACTATGACGGAACACTTTCACCGATTGTGGACAATCCTGAAAATGCATTAATGTCTGATGAGgtatgttttc ... gtattcacagATGCGTGCTGCAGTGAGGCATGCGGCATCACTTTTCCCAACTGCAATCATTAGCGGAAGATCTCGTGATAAG