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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctatttggacaaattatgttgtttgagctagaaatttagaatctaatttctctctattccattttttgatgatgaacaaaactttttttttcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAGATATGGCAGGAGCTTTCTAAAGCAAAATACATCGAATGGGAGAGCTTAT

Basic information

species Zea mays
transcript GRMZM2G104769_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104769_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g02140.3 (Oryza sativa), 3'ss of exon 4
-----ctatttggacaaattatg-ttgtttgagctagaa-atttagaatctaatttctctctattccattttttgatgatgaacaaaactttttttttcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAGATATGGCAGGAGCTTTCTAAAGCAAAATACATCGAATGGGAGAGCTTAT
      | ||||  |   || |  ||| |   ||||    | ||| ||   || ||||   ||  |||||||    |||||| | || ||||  |     || | |||| |||||||||||||||||||||||||| ||||| ||||||||||||||||| ||||| ||||||||||||||||||||||| |||||||| |  ||||
acttgttttttgtgcttgttcttcttgatgatgctattttagttacaactcaaattctgcttacgccattttac--tgatgatccaatctttact-----aacccagTCGTTGGAGCTTGGAAGGGGTGCACATCCAGCAAGTTACATGGTTGAAGAGATCTGGCAAGAGCTTTCTAAAGCAAAATACATAGAATGGGAAAATTTAT

upper sequence: GRMZM2G104769_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT3G07370.1 (Arabidopsis thaliana), 3'ss of exon 4
ctatttg-gacaaattatgttgtttgagctagaaatt--tagaatctaatttctctctatt--ccattttttgatga-tgaacaaaactttttttttcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAGATATGGCAGGAGCTTTCTAAAGCAAAATACATCGAATGGGAGAGCTTAT
  | | | ||    ||   ||||||  || |  || |  |  || | |||||   | |  |  |  |||  || | | |  |   | ||   |||   |    ||| | || || ||||||||  |  |  ||||  || | || ||||| ||||| |||||| | ||||||||||||||||||||||| || |||||     | |
--actagagatgggttggtttgtttatgccatcaaatactgcaaacaaattttggtttgatacctgtttcctgttaacttcatgtagctacgtttcata----tagGCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAGAAATATGGGAAGAGCTTTCTAAAGCAAAATACATGGAGTGGGAACTGGTTT
















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|76913822|gb|DV165266.1|DV165266
EST:     CTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAG                         TCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAG
genomic: CTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAGgtatcccctc ... tcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAG
EST: gi|211321469|gb|FL171487.1|FL171487
EST:     TCTTGTCAACGGCCAAAGATTATCAGAAGGAATAACATCACTGGAGAAAG                         -CCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGA
genomic: TCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAA-Ggtatcccctc ... tcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGA
EST: gi|211321468|gb|FL171486.1|FL171486
EST:     CTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAG                         TCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGC
genomic: CTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAGgtatcccctc ... tcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGC
EST: gi|94476727|gb|EB705685.1|EB705685
EST:     CTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAG                         TCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAG
genomic: CTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAGgtatcccctc ... tcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAG
EST: gi|211196887|gb|FL171483.1|FL171483
EST:     CTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAG                         TCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAAAG
genomic: CTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAGgtatcccctc ... tcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAG
EST: gi|71303900|gb|DR788068.1|DR788068
EST:     AAATCACTGGAGAAG                         TCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAG
genomic: AAATCACTGGAGAAGgtatcccctc ... tcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAG
EST: gi|61119637|gb|DN560598.1|DN560598
EST:     CTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAG                         TCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAG
genomic: CTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAGgtatcccctc ... tcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAG
EST: gi|211321467|gb|FL171485.1|FL171485
EST:     CTTGTNCA-CAGCCAAAGATTATCAGAAGGAAATAAA-TCACTGGAGAAG                         TCCTTGGAGCT-GGNAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGA
genomic: CTTGT-CAACAGCCAAAGATTATCAGAAGGAA-TAAAATCACTGGAGAAGgtatcccctc ... tcaaaactagTCCTTGGAGCTTGG-AAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGA
EST: gi|211321466|gb|FL171484.1|FL171484
EST:     CTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAG                         TCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACAT
genomic: CTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAGgtatcccctc ... tcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACAT
EST: gi|149106376|gb|EE292096.2|EE292096
EST:     CTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAG                         TCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAG
genomic: CTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAGgtatcccctc ... tcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAG
EST: gi|149106375|gb|EE292095.2|EE292095
EST:     GAAGGAATAAAATCACTGGAGAAG                         TCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAG
genomic: GAAGGAATAAAATCACTGGAGAAGgtatcccctc ... tcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAG
EST: gi|91054321|gb|EB164739.1|EB164739
EST:     CTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAG                         TCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAG
genomic: CTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAGgtatcccctc ... tcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAG

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: 38 (upstream exon), 49 (downstream exon)
Score: 17

GCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAGgtatcccctc ... tcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAGATATGGCAGGAGCTTTCTAAAGCAAAATACATCGAATGGGAGAGCTTAT


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

GCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAGgtatcccctc ... tcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAGATATGGCAGGAGCTTTCTAAAGCAAAATACATCGAATGGGAGAGCTTAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 32

GCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAGgtatcccctc ... tcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAGATATGGCAGGAGCTTTCTAAAGCAAAATACATCGAATGGGAGAGCTTAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 21

GCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAGgtatcccctc ... tcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAGATATGGCAGGAGCTTTCTAAAGCAAAATACATCGAATGGGAGAGCTTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttctctctattccattttttgatgatgaacaaaactttttttttcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAGATATGGCAGGAGCTTTCTAAAGCAAAATACATCGAATGGGAGAGCTTAT
                                    ctttttttttc  CT-rich tract
                             aacaaaactttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctatttggacaaattatgttgtttgagctagaaatttagaatctaatttctctctattccattttttgatgatgaacaaaactttttttttcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAGATATGGCAGGAGCTTTCTAAAGCAAAATACATCGAATGGGAGAGCTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - ggacaaa
- - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaaa