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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatataaaactcgatactcaggttttcataatttattgtgttgtttccagctctcaaaacatgttttgtttgcagATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGATGCGGAAGTGAGAGAGCTCGTTGAGAAGGCGTACGTGAGAGCGAAAGAGATCA

Basic information

species Arabidopsis thaliana
transcript AT5G42270.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g51029.1 (Oryza sativa), 3'ss of exon 4
-------------------gtaagtatataaaactcgatactcaggttttcataatttattgtgttgtttc-cagctctcaaaacatgttttgtttgcagATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGATGCGGAAGTGAGAGAGCTCGTTGAGAAGGCGTACGTGAGAGCGAAAGAGATCA
                    |   | |   ||  || ||   ||  |  |  ||  |   ||  | ||  |       |    | ||  |||| |||||||||||    |||||||| ||||||||||| || |||||||| || ||||| || ||||| |||||||| |||||||| |||   ||||| |   ||||||
tgtctaacctgcgttggttttgcttctcggaatttctatcggcaattcgtagtatctgtgtgaatggtagcatgatatttttcatatcctttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCTGAGGTGAGGGAGCTCGTGGAGAAGGCCTACTCAAGAGCAACGCAGATCA

upper sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G126361_T03 (Zea mays), 3'ss of exon 5
--------gtaagtatataaaactcgatactcaggttttcataatttattgtgttgtttccag-------ctctcaaa-----acatgttttgttt-gcagATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGATGCGGAAGTGAGAGAGCTCGTTGAGAAGGCGTACGTGAGAGCGAAAGAGATCA
        |  |||||  || | | |   | ||  | |||| ||||  | |      ||  |        ||  ||||     |||| ||||      |||||||||   |||||||| ||||| ||||||||||||||||| || || || || ||||| || ||||| |||||||| |||   ||||| |   |||| |
ctctcttagccagtatg-aatagtagtcgcacaaatgttcacaattcctagcaccagtttgaagagcaatctgacaaatattcacattttttcccccacagATGTCAAGCCAGAAGGACTACTCTATGGCAACAGCGGATGTTGTGGACGCCGAGGTGAGGGAACTCGTGGAGAAGGCCTACTCTAGAGCAAGGCAGATAA

upper sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G02100.1 (Glycine max), 3'ss of exon 4
----gtaagtatataaaactcgatactcaggttttcataatttattgtgttgtttccagctctcaaaacatgtt------------------ttgtt-tgcagATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGATGCGGAAGTGAGAGAGCTCGTTGAGAAGGCGTACGTGAGAGCGAAAGAGATCA
    |  |  |  |||||   | |  ||    ||| | | | ||    |||| |         ||||| || |                   ||||  |||||||||||||||| ||||||||||| |||||||| |||||||| || |||||||||||||| || || || ||||  || ||    || || | | | || |
gtatgctatgacctaaaataggttgatcc--cttttacactgtaa-acgttgctcttgaacaccaaaatatatgcctgaccatttcaaatgattgtaatgcagATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCGGAAGTGAGGGAACTGGTAGAGAGAGCATATTCTAGGGCAACACATATTA

upper sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G02200.1 (Glycine max), 3'ss of exon 4
---------------------gtaagtatataaaactcgatactcag-gttttcataatttattgtgttgtttccagctctcaaaacatgttttgtttgcagATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGATGCGGAAGTGAGAGAGCTCGTTGAGAAGGCGTACGTGAGAGCGAAAGAGATCA
                      |   |   |   ||    ||  | | ||| |   |    | ||| |   | ||    |     | ||| ||     ||||||||||||||| ||||||||||| |||||||| |||||||| || |||||||||||||| || || || ||||  || ||    || || | | | || |
gtatgccatgacctataacagattgatgccttttacaatgtaaacggtgttcttcaacaccaatgtatatatgcctcaccctgtcaaatgattgtaacgcagATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCGGAAGTGAGGGAACTGGTAGAGAGAGCATATTCTAGGGCAACACATATTA

upper sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0001g00190.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtatataaaactcgatactcaggttttcataatt------tattgtgttgtttccagctct--caa-----aacatgttt--tgttt------gcagATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGATGCGGAAGTGAGAGAGCTCGTTGAGAAGGCGTACGTGAGAGCGAAAGAGATCA
||| | | |||      |||| |  | | | |  || |      |    ||   ||     |  |  |||     ||||| |||  |||||      |||||||||||||||||| || || || |||||||| || ||| | || |||||||||||||| ||| | || |||||||| ||    ||||| ||  ||||||
gtaggaacatattttaagatattttgctctccccaagtgtggagtcccatgcgattcatcaccttaccaagattgaacatttttggtgtttcaaatggcagATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCGGAAGTGAGGGAGTTGGTGGAGAAGGCATATTCAAGAGCCAAGCAGATCA

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|125301077|gb|EL315162.1|EL315162
EST:     AGTTGGTGGAGCAGGAGGAAACCCTTTCTTGGGTCTAAAGT                         ATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGAT
genomic: AGTTGGTGGAGCAGGAGGAAACCCTTTCTTGGGTC-AAAGTgtaagtatat ... ttgtttgcagATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGAT
EST: gi|124987661|gb|EL060104.1|EL060104
EST:     ACAAGTTGCAGTTGGTGGAGCAGGAGGAAACCCTTTTCTTGGGTCAAAGT                         ATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGG
genomic: ACAAGTTGCAGTTGGTGGAGCAGGAGGAAACCCTTT-CTTGGGTCAAAGTgtaagtatat ... ttgtttgcagATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGG
EST: gi|125266412|gb|EL280497.1|EL280497
EST:     TGCAGTTGGTGGAGCAGGAGGAAACCCTTTCTTGGGTCAAAGT                         ATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGATGCG
genomic: TGCAGTTGGTGGAGCAGGAGGAAACCCTTTCTTGGGTCAAAGTgtaagtatat ... ttgtttgcagATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGATGCG
EST: gi|124937329|gb|EL014111.1|EL014111
EST:     ACAAGTTGCAGTTTGGTGGAGCAGGAGGAAACCCTTTCTTGGGTCAAAGT                         ATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGA
genomic: ACAAGTTGCAG-TTGGTGGAGCAGGAGGAAACCCTTTCTTGGGTCAAAGTgtaagtatat ... ttgtttgcagATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGA
EST: gi|125271010|gb|EL285095.1|EL285095
EST:     TGCAGTTGGTGGAGCAGGAGGAAACCCTTTCTTTGGGTCAAAGT                         ATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGATGCG
genomic: TGCAGTTGGTGGAGCAGGAGGAAACCCTTTC-TTGGGTCAAAGTgtaagtatat ... ttgtttgcagATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGATGCG
EST: gi|124794579|gb|EH884258.1|EH884258
EST:     GAAACCCTTTCTTGGGTCAAAGT                         ATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGATGCG
genomic: GAAACCCTTTCTTGGGTCAAAGTgtaagtatat ... ttgtttgcagATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGATGCG
EST: gi|124796861|gb|EH886540.1|EH886540
EST:     GGAGGAAACCCTTTCTTCGGGTCAAAGT                         TTGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGATGCG
genomic: GGAGGAAACCCTTTCTT-GGGTCAAAGTgtaagtatat ... ttgtttgcagATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGATGCG
EST: gi|124823953|gb|EH908819.1|EH908819
EST:     GACAAGTTGCAGTTGGTGGAGCAGGAGGAAACCCTTTCTTGGGTCAAAGT                         ATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTG
genomic: GACAAGTTGCAGTTGGTGGAGCAGGAGGAAACCCTTTCTTGGGTCAAAGTgtaagtatat ... ttgtttgcagATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttttcataatttattgtgttgtttccagctctcaaaacatgttttgtttgcagATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGATGCGGAAGTGAGAGAGCTCGTTGAGAAGGCGTACGTGAGAGCGAAAGAGATCA
                                           ttttgttt  CT-rich tract
       ataatttattgtgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatataaaactcgatactcaggttttcataatttattgtgttgtttccagctctcaaaacatgttttgtttgcagATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGATGCGGAAGTGAGAGAGCTCGTTGAGAAGGCGTACGTGAGAGCGAAAGAGATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA