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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgagctctttgataaaatctcaatttagtgtgagccttatatatgtgttttctctgtaaaatcttgttgattaggtccctatcatttttctttcaacagCCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGATCCAGCGGTCTTCACCGGAGATACCTTG

Basic information

species Zea mays
transcript GRMZM2G031825_T05
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031825_T05 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g21460.1 (Oryza sativa), 3'ss of exon 3
ttgagctctttgataaaatctcaatttagtgtgagccttatatatgtgttttctctgtaaaatcttgttgattaggt-----------ccctatcattt---ttctttcaacagCCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGATCCAGCGGTCTTCACCGGAGATACCTTG
    |  | ||| |   |   || | ||||   | |||| |||||||      ||||||| | |||||||||||  |            ||| ||||||   |||||  ||||||||||| ||||| ||||||||||| || || |||||||| ||||  ||||||||||| || || || ||||| ||||||
----gtgcattggttgta---cagtctagtc--aaccttttatatgt-----ttctgtaacagcttgttgattacttaaatctcatagtcctttcatttcccttcttctaacagCCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTG
















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|60343728|gb|DN210701.1|DN210701
EST:     AAGTTGTCACTTGGGAAGGACATTGAGATACTATGCCTACACACGCCTTG                         CCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGA
genomic: AAGTTGTCACTTGGGAAGGACATTGAGATACTATGCCTACACACGCCTTGgtatgctgtt ... ctttcaacagCCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGA
EST: gi|60352510|gb|DN219483.1|DN219483
EST:     AAGTTGTCACTTGGGAAGGACATTGAGATACTATGCCTACACACGCCTTG                         CCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGA
genomic: AAGTTGTCACTTGGGAAGGACATTGAGATACTATGCCTACACACGCCTTGgtatgctgtt ... ctttcaacagCCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGA
EST: gi|32857618|gb|CD997299.1|CD997299
EST:     AAGTTGTCACTTGGGAAGGACATTGAGATACCATGCCTACACACGCCTTG                         CCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGA
genomic: AAGTTGTCACTTGGGAAGGACATTGAGATACTATGCCTACACACGCCTTGgtatgctgtt ... ctttcaacagCCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGA
EST: gi|32930530|gb|CF035342.1|CF035342
EST:     AAGTTGTCACTTGGGAAGGACATTGAGATACTATGCCTACACACGCCTTG                         TCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGA
genomic: AAGTTGTCACTTGGGAAGGACATTGAGATACTATGCCTACACACGCCTTGgtatgctgtt ... ctttcaacagCCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGA
EST: gi|71430487|gb|DR811537.1|DR811537
EST:     AAGTTGTCACTTGGGAAGGACATTGAGATACTATGCCTACACACGCCTTG                         CCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGA
genomic: AAGTTGTCACTTGGGAAGGACATTGAGATACTATGCCTACACACGCCTTGgtatgctgtt ... ctttcaacagCCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGA
EST: gi|60345729|gb|DN212702.1|DN212702
EST:     ATGCCTACACACGCCTTG                         CCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGA
genomic: ATGCCTACACACGCCTTGgtatgctgtt ... ctttcaacagCCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGA
EST: gi|34391313|gb|CF384541.1|CF384541
EST:     AAGTTGTCACTTGGGAAGGACATTGAGATACTATGCCTACACACGCCTTG                         CCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGA
genomic: AAGTTGTCACTTGGGAAGGACATTGAGATACTATGCCTACACACGCCTTGgtatgctgtt ... ctttcaacagCCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGA
EST: gi|51592666|gb|CV071812.1|CV071812
EST:     AAGTTGTCACTTGGGAAGGACATTGAGATACTATGCCTACACACGCCTTG                         CCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGA
genomic: AAGTTGTCACTTGGGAAGGACATTGAGATACTATGCCTACACACGCCTTGgtatgctgtt ... ctttcaacagCCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttttctctgtaaaatcttgttgattaggtccctatcatttttctttcaacagCCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGATCCAGCGGTCTTCACCGGAGATACCTTG
                    tgttgat  putative branch site (score: 4)
                               tccctatcatttttct  putative PPT
                                   tatcatttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgagctctttgataaaatctcaatttagtgtgagccttatatatgtgttttctctgtaaaatcttgttgattaggtccctatcatttttctttcaacagCCACACTAAAGGTCATATCAGCTACTATGTTACTAGTAAGGAGGGTGAAGATCCAGCGGTCTTCACCGGAGATACCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT