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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcacctttgctctagcttcctcaaagtattccagacttttttttgacatagttgaataatctgtatgttgaatggtctattgatttttcaccagATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAG

Basic information

species Zea mays
transcript GRMZM2G073774_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 6
gttcacctttgctctagcttcctcaaagtattccagacttttttttgacatagttgaataatctgtatgttgaatggtctattgatttttcaccagATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAG
  | | ||   |  |  || ||| |   |  | || ||        |||| | || | | |||| |||||| ||     |  ||||||||  | |||||||||| ||||||||||||||||||||||  || ||||| ||||||||||| |||||||| |||||||||||||| |||
-gttaactagacctt--ctaccttagctttcttcataccgca----gacacatttca-tcatctctatgttaaaattgttgatgatttttt-ctagATTACTCCAGCAAAGGATGGAAAACCTGTGCAGATTGAGCTCATTGATGCAAAAACAAAGGAACACAAAGAAACCCTCGAG

upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 6
gttcacctttgctctagcttcctcaaagtattccagacttttttttgacatagttgaataatctgtatgttgaatggtct---attgatttttcaccagATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAG
||   ||| |  | |       |  || || | |   || ||| |  | | |||      || | |   |    |   ||   ||  ||| ||   ||||||||||| |||| |||||| ||||| || || || |||||||||||||| || || ||||| |  || || ||  | |||
gtgagcctgttatatcatgcattgcaaatactgctt-ctctttctctatacagtgtgtccatgtattcatctgttaaacttaaatctattcttattcagATTACTCCGGCAAGGGATGGGAAACCAGTTCTGATTGAGCTTATTGATGCCAAAACCAAGGAACCTAAGGATACTTTGGAG

upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 6
gttcacctttgctctagcttcctcaaagtattccagacttttttttgacatagttgaataatctgtatgttgaatggtctattgatttttcaccagATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAG
||      | ||||     || ||     |||  | | ||     |   |||   |   ||| | | | || ||||          || | || |||||||||| || |||||||||||||||||  | || || || |||||||||||||||||||| |  || || ||  | |||
gtgtttgatggctcacagctcttctttcaattgtaaaattaggaatagtataacagttaaatttctttctttaatg---------cttgttac-agATTACTCCAGCTAAGGATGGAAAACCTGTTATGATTGACCTCATTGATGCAAAGACAAAGGAACCAAAGGATACTTTAGAG

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|211514676|gb|FL210540.1|FL210540
EST:     TTATCAATCCTCGGAAAATTGACTATCACACTGGTGTTTTTGCAAGCAAG                         ATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCA
genomic: TTATCAATCCTCGGAAAATTGACTATCACACTGGTGTTTTTGCAAGCAAGgttcaccttt ... ttttcaccagATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCA
EST: gi|67016819|gb|CO445568.1|CO445568
EST:     TTATCAATCCTCGGAAAATTGACTATCACACTGGTGTTTTTGCAAGCAAG                         ATTACTCCTGCAAAGGATGGGAAACCTGTGCTCATCGAGCTTATTGATGCA
genomic: TTATCAATCCTCGGAAAATTGACTATCACACTGGTGTTTTTGCAAGCAAGgttcaccttt ... ttttcaccagATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCA
EST: gi|6536537|gb|AW224850.1|AW224850
EST:     TTATCAATCCTCGGAAAATTGACTATCACACTGGTGTTTTTGCAAGCAAG                         ATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCA
genomic: TTATCAATCCTCGGAAAATTGACTATCACACTGGTGTTTTTGCAAGCAAGgttcaccttt ... ttttcaccagATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCA
EST: gi|31354606|gb|CD438963.1|CD438963
EST:     TTATCAATCCTCGGAAAATTGACTATCACACTGGTGTTTTTGCAAGCAAG                         ATTACTCCTGCAAAGGATGGGAAACCTGTGCTCATCGAGCTTATTGATGCA
genomic: TTATCAATCCTCGGAAAATTGACTATCACACTGGTGTTTTTGCAAGCAAGgttcaccttt ... ttttcaccagATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCA
EST: gi|6626525|gb|AW258057.1|AW258057
EST:     TTATCAATCCTCGGAAAATTGACTATCACACTGGTGTTTTTGCAAGCAAG                         ATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCA
genomic: TTATCAATCCTCGGAAAATTGACTATCACACTGGTGTTTTTGCAAGCAAGgttcaccttt ... ttttcaccagATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCA
EST: gi|32932110|gb|CF036922.1|CF036922
EST:     TTATCAATCCTCGGAAAATTGACTATCACACTGGTGTTTTTGCAAGCAAG                         ATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCA
genomic: TTATCAATCCTCGGAAAATTGACTATCACACTGGTGTTTTTGCAAGCAAGgttcaccttt ... ttttcaccagATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCA
EST: gi|31353176|gb|CD437533.1|CD437533
EST:     TTATCAATCCTCGGAAAATTGACTATCACACTGGTGTTTTTGCAAGCAAG                         ATTACTCCTGCAAAGGATGGGAAACCTGTGCTCATCGAGCTTATTGATGCA
genomic: TTATCAATCCTCGGAAAATTGACTATCACACTGGTGTTTTTGCAAGCAAGgttcaccttt ... ttttcaccagATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCA

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: 49 (upstream exon), 49 (downstream exon)
Score: 192

GCTGATGCCTGGATTTGATCCTGAAATTGCAAAATTAGCCCAGAGAGTTCTTATCAATCCTCGGAAAATTGACTATCACACTGGTGTTTTTGCAAGCAAGgttcaccttt ... ttttcaccagATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

GCTGATGCCTGGATTTGATCCTGAAATTGCAAAATTAGCCCAGAGAGTTCTTATCAATCCTCGGAAAATTGACTATCACACTGGTGTTTTTGCAAGCAAGgttcaccttt ... ttttcaccagATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

GCTGATGCCTGGATTTGATCCTGAAATTGCAAAATTAGCCCAGAGAGTTCTTATCAATCCTCGGAAAATTGACTATCACACTGGTGTTTTTGCAAGCAAGgttcaccttt ... ttttcaccagATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 290

GCTGATGCCTGGATTTGATCCTGAAATTGCAAAATTAGCCCAGAGAGTTCTTATCAATCCTCGGAAAATTGACTATCACACTGGTGTTTTTGCAAGCAAGgttcaccttt ... ttttcaccagATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgacatagttgaataatctgtatgttgaatggtctattgatttttcaccagATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAG
                                      tattgat  putative branch site (score: 290)
                                            tttttcacc  CT-rich tract
                                      tattgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcacctttgctctagcttcctcaaagtattccagacttttttttgacatagttgaataatctgtatgttgaatggtctattgatttttcaccagATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA