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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGATTAGCCACAGGACGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCGgttcgtttcctgtcgctctctcctttgttggagcttcacaagttacgctgatggtgcatgtccatgaatggtgcttgatggtttctcggattgtgcag

Basic information

species Zea mays
transcript GRMZM2G074401_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074401_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g18070.1 (Oryza sativa), 5'ss of exon 3
GAGGATTAGCCACAGGACGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCGgttcgtttcctgtcgctctctcctttgttggagcttcacaagttacgctgatggtgcatgtccatgaatggtgcttgatggtttctcggattgtgcag
|||||||||||||||||||||||| || |||||||| || || ||||| |||||||||||||| |||||  || |  |||   |   |  ||  |  |   |||   | ||  |||   | ||  | || |    ||          |                 
GAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGACGAGTCCTGGCAACCGgtaggtctt-tgtttttggttggttcatgaggaattctgcaattttgct--cgatggttctctaatcgtgacaacctgcag-----------------

upper sequence: GRMZM2G074401_T01 (Zea mays), 5'ss of exon 3
lower sequence: EDP09401 (Chlamydomonas reinhardtii), 5'ss of exon 5
------GAGGATTAGCCACAGGACGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCGgttcgtttcctgtcgctctctcctttgttggagcttca--caagtt----acgctg-atggtgcatgtccatgaatggtgcttgatggtttctcgg-attgtgcag----------------------------------------------------------------------------------------------------------------
      | | || |||||| | || |||||    |||||||||||||||||||| |||||||| |||||||| ||         |  |  |   |   || |||  ||  |  || ||      ||| | | | |  |  |    | |   |||||||  |    | ||  |   || |                                                                                                                
CGGCTGGCGCATCAGCCACCGCACTCACCACGCCAACCACGGCCACGTTGAGAACGACGAGTCGTGGCACCCCGTGACCAAGAAGCTGTACGACCACCTGgtgggtctcgagccatgtctgaagcgcagcaggattgacattggagcaaaatgcttgactgccattaggcgtcaggcggtagcatcgttccaccggcctcggtgctactggttaactctgctgctggtcccgacggtaacgcaccagaaacatactttatctcttatgccctctgctttcttgaactgcag

upper sequence: GRMZM2G074401_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S98_209V6.1 (Physcomitrella patens), 5'ss of exon 3
GAGGATTAGCCACAGGACGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCGgttcgtttcctg--tcgctctctcctttgttggagcttcacaagttacgctgat--ggtgcatgtccatgaatggtgcttgatg-gtttctcggattg-tgcag-------------
| | |||||||||||||| ||||| || |||||||| ||||| ||||| |||||||| ||||| || || ||| || ||  |||||     |    | |  | |  | | |     |||||  ||      ||||   || |||  |   |  || |||  |||  ||  |             
GCGCATTAGCCACAGGACTCACCACCAGAACCACGGGCACGTGGAGAACGACGAGTCATGGCATCCTgtacgtctcttgaatcgctgggagcaaaatagttggtcgaaatgagcatctgatttggaagcaatccagacattgtgtatttcgtattactctaattactgttgatgactattgcag

upper sequence: GRMZM2G074401_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 3
GAGGATTAGCCACAGGACGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCGgttcgtttcctgtcgctctctcctttgttggagcttcacaagttacgctgatggtgcatgtccatgaatggtgcttgatggtttctcggattgtgcag
|||||| |||||| ||||||| || || || |||||||| || ||||| |||||||||||||| || ||  ||  |||   |||||  |    ||   | |        ||   || ||  | ||      |  |||  |                         
GAGGATAAGCCACCGGACGCATCACCAGAATCACGGCCATGTCGAGAACGACGAGTCCTGGCATCCAgtaagtcgccttaagctcttcca--agtgaaaaccatttcgtttttccttatcttacactgttcttcatgtag-------------------------

upper sequence: GRMZM2G074401_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ20170 (Selaginella moellendorffii), 5'ss of exon 3
GAGGATTAGCCACAGGACGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCGgttcgtttcctgtcgctctctcctttgttggagcttcacaagttacgctgatggtgcatgtccatgaatggtgcttgatggtttctcggattgtgcag
|||||| |||||| ||||||| || || || |||||||| || ||||| |||||||||||||| || ||  ||  ||||  |||||| |   ||    | | |      || | || |   | ||      |  |||  |                         
GAGGATAAGCCACCGGACGCATCACCAGAATCACGGCCATGTCGAGAACGACGAGTCCTGGCATCCAgtaagtcgcctgatgctctcgcaagtgg-aaaccattttgtttttctcttaccttacactgttcttcatgtag-------------------------

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|13515603|gb|BG517879.1|BG517879
EST:     CGTTGAGAAGGACGAGTCCTGGCACCCG                         CTACCAGAGAGGCTGTACAAAAGCCTGGACTTTATGACTAGGAAATTGCGG
genomic: CGTTGAGAAGGACGAGTCCTGGCACCCGgttcgtttcc ... gattgtgcagCTACCAGAGAGGCTGTACAAAAGCCTGGACTTTATGACTAGGAAATTGCGG
EST: gi|60401022|gb|DN233829.1|DN233829
EST:     CGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCG                         CTACCAGAGAGGCTGTACAAAAGCCTGGACTTTATGACTAGGAAATTGCGG
genomic: CGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCGgttcgtttcc ... gattgtgcagCTACCAGAGAGGCTGTACAAAAGCCTGGACTTTATGACTAGGAAATTGCGG
EST: gi|32939492|gb|CF044311.1|CF044311
EST:     CGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCG                         CTACCAGAGAGGCCGTACAAAAGCCTGGACTTTATGACTAGGAAATTGCGG
genomic: CGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCGgttcgtttcc ... gattgtgcagCTACCAGAGAGGCTGTACAAAAGCCTGGACTTTATGACTAGGAAATTGCGG
EST: gi|32938850|gb|CF043669.1|CF043669
EST:     CGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCG                         CTACCAGAGAGGCTGTACAAAAGCCTGGACTTTATGACTAGGAAATTGCGG
genomic: CGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCGgttcgtttcc ... gattgtgcagCTACCAGAGAGGCTGTACAAAAGCCTGGACTTTATGACTAGGAAATTGCGG
EST: gi|148965401|gb|EE016203.2|EE016203
EST:     CGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCG                         CTACCAGAGAGGCTGTACAAAAGCCTGGACTTTATGACTAGGAAATTGCGG
genomic: CGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCGgttcgtttcc ... gattgtgcagCTACCAGAGAGGCTGTACAAAAGCCTGGACTTTATGACTAGGAAATTGCGG

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: 47 (upstream exon), 48 (downstream exon)
Score: 26

GAGGATTAGCCACAGGACGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCGgttcgtttcc ... gattgtgcagCTACCAGAGAGGCTGTACAAAAGCCTGGACTTTATGACTAGGAAATTGCGGTTCACCATGCCGTTCCCCTTGCTCGCATTCCCGTTATACTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 126

GAGGATTAGCCACAGGACGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCGgttcgtttcc ... gattgtgcagCTACCAGAGAGGCTGTACAAAAGCCTGGACTTTATGACTAGGAAATTGCGGTTCACCATGCCGTTCCCCTTGCTCGCATTCCCGTTATACTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 41

GAGGATTAGCCACAGGACGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCGgttcgtttcc ... gattgtgcagCTACCAGAGAGGCTGTACAAAAGCCTGGACTTTATGACTAGGAAATTGCGGTTCACCATGCCGTTCCCCTTGCTCGCATTCCCGTTATACTTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 122

GAGGATTAGCCACAGGACGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCGgttcgtttcc ... gattgtgcagCTACCAGAGAGGCTGTACAAAAGCCTGGACTTTATGACTAGGAAATTGCGGTTCACCATGCCGTTCCCCTTGCTCGCATTCCCGTTATACTTG