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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctataagtagtgaggcttatgtcagtcattgcgtgcagcacttggcatgcattttttgattctatacattcttaatttgcctcgtactctttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG

Basic information

species Zea mays
transcript GRMZM2G068255_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068255_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g45240.2 (Oryza sativa), 3'ss of exon 2
--tctataagtagtgaggcttatgtcagtcattgcgtgcagcacttggcat--gcattttttgattctatacattcttaatttgc-ctcgtactctttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG---
  ||  |   | |||    ||||||       ||    ||| | |    ||  | |||| ||||  ||   |||    ||||||  ||  ||| |||| |||||||||||| |||||||||| ||||||||||| ||||| |||||||||||||||||||||||||||||||| || |||| |||||| ||||| |||||||   
cctccctccct-gtgtttgttatgttttcttatgtacacagtagtacttattggtatttcttgaggctggccat----aatttgtacttttaccctttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGCTTTTCAAACCCTACTGACCTTGCTGGAGCAATTAAAGAAATGAATGGTT

upper sequence: GRMZM2G068255_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g45240.4 (Oryza sativa), 3'ss of exon 2
--tctataagtagtgaggcttatgtcagtcattgcgtgcagcacttggcat--gcattttttgattctatacattcttaatttgc-ctcgtactctttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG
  ||  |   | |||    ||||||       ||    ||| | |    ||  | |||| ||||  ||   |||    ||||||  ||  ||| |||| |||||||||||| |||||||||| ||||||||||| ||||| |||||||||||||||||||||||||||||||| || |||| |||||| ||||| |||||||
cctccctccct-gtgtttgttatgttttcttatgtacacagtagtacttattggtatttcttgaggctggccat----aatttgtacttttaccctttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGCTTTTCAAACCCTACTGACCTTGCTGGAGCAATTAAAGAAATGAATG

upper sequence: GRMZM2G068255_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G36570.1 (Glycine max), 3'ss of exon 3
tctataagtag-tgaggcttatgtcagtcat-tgcgtgcagcacttggcatgcattttt-tgattctatacattcttaatttgcctcgtactctttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG
    |||| |       ||| | | | | || ||  ||  |  | ||   | | || |  ||  |  | |   |  | |||    |     | | |     ||||||| ||||| ||| ||||||| ||||| ||||| |||||||||||||||||| | || ||| |||| || ||||| ||  | ||||| |||||||
---ctaagcaaacttaacttttattatttatgtgtttgtggtgcatgtatttccttgtgatgtgttgacagtgttgtgattaaggtatgtttatcttgactagGTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTTCTGACCTTGCTGCTGCTCTTAAAGAAATGAATG

upper sequence: GRMZM2G068255_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G01300.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------tctataag-tagtgaggcttatgtcagtcattgcgtgcagcacttggcat--gcattttttgattctatacattcttaatttgcc----tcgtactc--tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG
                                                                         |||||    |  | ||  || |||   | |  |     ||   ||   ||  |  | | || |       | | ||||||   |     |  |  |   | |  |  ||||||| ||||||||  ||||||| ||||| ||||| |||||||||||||||||| | || ||| |||| || ||||| ||  | ||||| |||||||
gtaagtggattactcatctagctcaaatgatttttatgtttaggaatgattgtggtgcttctgtgagcatttttctatttcctcttcagatttttgtt--tgaagggacagagttgttaatatttgtgtatcttaacgtaggtcttgcttaatgacctgaagttatgtttgatcttgtctagGTTGTCAGAGATAAACGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATG

upper sequence: GRMZM2G068255_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G30900.2 (Glycine max), 3'ss of exon 3
tctataagtagtgaggcttatgtcagtcattgcgtgcagcacttggcatgcattttt-tgattctatacattcttaatttgcctcgtactctttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG
 ||| |   | | |   ||   |   | | ||  ||  |  | ||   | | || |  ||| |  | |   |  | |||    |     | | |     ||||||| ||||| ||| ||||||| ||||| ||||| |||||||||||||||||| | || ||| |||| || ||||  ||  | ||||| |||||||
-ctaaacaaacttaacgtttattatttaagtgtttgtggtgcatgtatttccttgtaatgagttgacagtgttgtgattaaggtatgtttatcttgactagGTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG

upper sequence: GRMZM2G068255_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G04500.1 (Arabidopsis thaliana), 3'ss of exon 3
tctataagtagtgaggcttatgtcagtcattgcgtgcagcacttggcatgcattttttgattctatacattctt----aatttgcctcgtactctttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG
   ||| |   | |  ||||    | |||    |   || | |  |  |   |||| || |   |  | | |      |||  |  || || |    ||  |||||  ||||||||||| ||||||| ||||| || || ||||| |||||||| || | ||| ||| | ||||| || |||||  ||||||| |||||||
---atacg-gatcattcttactcgaatcacaaagataagtattcagtgttagttttgtggtcaaactcgtaccagaaaaataagagtcttatttaccatgacagGTCATTAGAGATAAGCGGACTGGTAAAACCAAGGGTTATGGGTTTGTGAGTTTCTTAAATCCTGCGGATCTAGCAGCAGCCTTAAAAGAAATGAATG

upper sequence: GRMZM2G068255_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv14s0036g00630.t01 (Vitis vinifera), 3'ss of exon 3
--tctataagtagtgaggctta-tgtcagtcattgcgtgcagcacttggcatg-cattttttgattctatacattcttaatttgcctcgtactctttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG
   || | |      |||||   ||| | |  ||      || ||||| |||  || |||||     |  | | |  |   | |   |  || ||      |||||||| ||||||||| |||| || ||||| |  |||||||||||||| |||||||| ||||||   || || || |||||| | || || ||||| |
ttactgtgatcttgcaggctggctgttaattttttgaatgaggacttgtcatatcactttttatggttggaaactaatgcatagttcctcacactca----cagGTTGTCAGAGATAAGCGGACAGGAAAAACCAGGGGCTATGGATTTGTTAGCTTTTCCAACCCTTTAGACCTTGCAGCAGCACTTAAGGAAATGAACG

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|211002219|gb|FL464441.1|FL464441
EST:     TTCCATCGTTCAACATGGCAAGG                         GTTGTTAGAGATAAGAGTACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
genomic: TTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
EST: gi|78080540|gb|DV508952.1|DV508952
EST:     ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGG                         GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
genomic: ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
EST: gi|31612073|gb|CD568695.1|CD568695
EST:     ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGG                         GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
genomic: ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
EST: gi|71320385|gb|DR796941.1|DR796941
EST:     ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGG                         GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
genomic: ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
EST: gi|31612074|gb|CD568696.1|CD568696
EST:     ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGG                         GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
genomic: ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
EST: gi|13150735|gb|BG321057.1|BG321057
EST:     ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTTAACATGGCAAGG                         GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
genomic: ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
EST: gi|60353545|gb|DN220518.1|DN220518
EST:     ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGG                         GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
genomic: ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
EST: gi|78083193|gb|DV511586.1|DV511586
EST:     ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGG                         GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
genomic: ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
EST: gi|60397448|gb|DN230264.1|DN230264
EST:     CTCTCCAAAGCATTTTCACGGTTTCCATCCTTTAACATGGCAAGG                         GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
genomic: CTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
EST: gi|74235772|gb|DT643686.1|DT643686
EST:     ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGG                         GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
genomic: ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
EST: gi|89248698|gb|DY620484.1|DY620484
EST:     ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGG                         GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
genomic: ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgcattttttgattctatacattcttaatttgcctcgtactctttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG
                         tcttaat  putative branch site (score: 3)
                                          ctctttatttc  putative PPT
      attttttgattctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctataagtagtgaggcttatgtcagtcattgcgtgcagcacttggcatgcattttttgattctatacattcttaatttgcctcgtactctttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - -gcttatg
- - - - - - - - - - - - - - - tgcgtgc
- - - - - - - - - - - - - - - - - - - gcacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcctcg