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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttcatcatgctattgattcttccaccgcctcatgtgaaaaactcagttacagaatttattttgaattgcag

Basic information

species Zea mays
transcript GRMZM2G044027_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 6
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttcatc--atgct-attgattcttccaccgc--ctcatgtgaaaaactcagttacagaa----tttattttgaattgcag
|||||||||||||| ||||| || |||||||||||||| || ||||| ||||||||||||||||||| ||||| | ||||| ||| | | ||| || || ||| ||| | | | | | | ||||| ||| | |||||
ACCATCAAGACAAACGTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAGgttggtgtttttttaatgctgattaacttgtcctatgcaacttatgagaactatataatgaagggaggtttttatgttgtactgcag

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA11G15020.1 (Glycine max), 5'ss of exon 6
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgt-tcatcat--gctattgattcttccaccgcctcatgtgaaaaactcagttacagaatttattttgaattgcag-----------------------
|| || ||||||||||| ||||| || ||||||||||| || |||||||| ||||||| || |||| | | || | | | |||| || || | || | | || ||| ||| |||| | | |
ACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAACGAGTTGGGGCAAGgttggaaaattgtctttggaaaatgataatttcagcttctatcatcatttggtct-ttattctttttctttttagtagagtcttagttcttattttattggcag

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA12G06990.1 (Glycine max), 5'ss of exon 6
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgt-tcatcat--gctattgattcttccaccgcct--catgtgaaaaactcagttacagaatttattttgaattgcag------------------
|| || ||||||||||| |||||||| ||||||||||| || ||||| ||| ||||||| || |||| || | || | | | |||| || || | || ||| | || || || || | | | ||
ACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAGgttggtaaattgtctttggaaaatgataatttcagcttctatcatcagttggtctttattctttttcttcttgttagtcttagttcttattttattggcag

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA13G40960.1 (Glycine max), 5'ss of exon 7
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttcatcatgctattgattcttccaccgcc-tcatgtgaaaaactcagttacagaatttattttgaattgcag
|| || ||||||||||| ||||| || ||||||||||| || ||||||||| |||| ||||| |||| | | | | | || || || ||| | || | ||| | || ||| | | |||
ACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAGgttgggatattttcttaaacaataatctcaactgctgccattagttggtcttaatta---gttctaattttattgacag

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 6
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcag--------tgttcatcatgctattgattcttccaccgcctcatg-tgaaaaactcagttacagaatttattttgaattgcag
|| || ||||||||||| ||||| ||| |||||||| |||| ||||| |||||||||||||| |||| | || | || | ||| | || ||| | || | ||| || || || | | |||
ACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAGgttggaaactacttgcccgtctctttgttgcattttgtttataaacataattctggtcttacttatagcatgtaataatggctacag

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 6
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 6
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgt-cagtgttcatcatgctattgattcttccac--cgcctcatgtgaaaaactcagttacagaattta---ttttgaattgcag----------------
||||||||||||||||| |||||||| || |||||||| || || || || ||||||| || |||| || ||| | | | |||| | | | | | || | | | | ||| ||| ||
ACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAGgtgcaaaattctttgtatatcttgctctttaatttctcttgtcaccaggaaactggcagctggacttacgatttcatgttatgtatactgcaagtagctc

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|6637013|gb|AW261285.1|AW261285
EST:     GTTATTGGTACCCTGAACATGCTGGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGNTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|149097834|gb|EE183762.2|EE183762
EST:     GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|32841175|gb|CD980856.1|CD980856
EST:     ACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
genomic: ACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|14206834|gb|BG840512.1|BG840512
EST:     GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|32909997|gb|CF014809.1|CF014809
EST:     GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|6194647|gb|AW146751.1|AW146751
EST:     GTTATTGGTACCCTGAACATGCTGGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGNGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|32841101|gb|CD980782.1|CD980782
EST:     ACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
genomic: ACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|6020952|gb|AW065880.1|AW065880
EST:     GTTATTGGTACCCTGAACATGCTGGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|211032180|gb|FL277400.1|FL277400
EST:     GTTATTGGTACCCTGAACATGCTGGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|32850262|gb|CD989943.1|CD989943
EST:     TACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
genomic: TACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|32850632|gb|CD990313.1|CD990313
EST:     ACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
genomic: ACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|32850126|gb|CD989807.1|CD989807
EST:     GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|32850554|gb|CD990235.1|CD990235
EST:     ACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
genomic: ACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|22473192|gb|BU037672.1|BU037672
EST:     GTTATTGGTACCCTGAACATGCTGGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCACTCGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|213173372|gb|FM186537.1|FM186537
EST:     GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|26558105|gb|CA830340.1|CA830340
EST:     GTTATTGGTACCCTGAACATGCTGGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGT
genomic: GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGT
EST: gi|32850616|gb|CD990297.1|CD990297
EST:     ACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
genomic: ACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|148945878|gb|EC891170.2|EC891170
EST:     GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|32840343|gb|CD980024.1|CD980024
EST:     ACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
genomic: ACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|32840626|gb|CD980307.1|CD980307
EST:     ACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
genomic: ACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|32849033|gb|CD988714.1|CD988714
EST:     ACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATTCGCTTGAGCATCC
genomic: ACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|67016223|gb|CO444972.1|CO444972
EST:     GTTATTGGTACCCTGAACATGCTGGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|67013235|gb|CO441984.1|CO441984
EST:     GTTATTGGTACCCTGAACATGCTGGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|21987903|gb|BQ779431.1|BQ779431
EST:     GTTATTGGTACCCTGAACATGCTGGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|32165003|gb|CD670321.1|CD670321
EST:     GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
EST: gi|148951041|gb|EC896695.2|EC896695
EST:     GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttc ... tgaattgcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAGgtcagtgttcatcatgctattgattcttccaccgcctcatgtgaaaaactcagttacagaatttattttgaattgcag

- - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT