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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaagattgtagtcatatcatttggatgcattggaaggctttgctaattgttttcctggtttctatcatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCAAAAGACTGGATTGATATGTTCAATGAACATGAAATTCAG

Basic information

species Zea mays
transcript GRMZM2G101098_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101098_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g06690.3 (Oryza sativa), 3'ss of exon 21
gtaaaaagattgtagtcatatcatttggatgcattggaaggctttgcta-attgttttcc----tggtttctatcatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCAAAAGACTGGATTGATATGTTCAATGAACATGAAATTCAG
|||| |  ||    |   | |||||||  ||  ||| ||  | ||| || ||  ||| ||    |  ||| ||||| ||||||| || ||||| ||||| || |||||||| |||||||| || ||||| || || |||||| | |||||||||||||||||| | |||
gtaatacaat----gcattgtcatttgcttgtcttgaaatacgttgatacataatttgccattgttttttttatcacagATCCGCGCCCAAAGCACACATTTTTTGAGAGGCTTTCAACAACTAATACCGAATGAATGGATTAACATGTTCAATGAACATGAATTCCAG

upper sequence: GRMZM2G101098_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G36390.1 (Glycine max), 3'ss of exon 20
--------------------------gtaaaaagattgtagtcatatcatttggatgcattggaaggctttgctaattgttttcctggtttctatcatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCAAAAGACTGGATTGATATGTTCAATGAACATGAAATTCAG
                            |    | || |    |   ||  |  |  |||        |    ||||  |  |  |  ||    |   |||| ||   ||||||| |||| |||||||| || ||||| || ||||| |  || || |||||||| ||||| |||||||||||| |||||
tatatactctatctctatctgatgtgacacttgggtttttccaaatgcaaatcaactcatgtttcaattacaataataataataataattatgttttcagATACGCCAACAAAGTTCACATTTCTTGAGGGGATTTCAGCAACTTATTCAGAAGGATTGGATTGACATGTTTAATGAACATGAACTTCAG

upper sequence: GRMZM2G101098_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G04180.1 (Glycine max), 3'ss of exon 20
-----------------------gtaaaaaga---ttgtagtcatatcatttggatgcattggaaggctttgctaattgttttcctggtttctatcatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCAAAAGACTGGATTGATATGTTCAATGAACATGAAATTCAG
                         |||  ||   |||   |  |  || |   |  ||    | |  |    ||     |    |  ||    |   |||| ||   ||||||| |||| |||||||| || ||||| || ||||| |  || || |||||||| ||||| |||||||||||| |||||
ctctattatggctctatctctagccaaagtgacacttgggttttttccaatgcaaatcaacccatgtttcaattacagaataaaataattatgttttcagATACGCCAACAAAGTTCACATTTCTTGAGGGGATTTCAGCAACTTATGCAGAAGGATTGGATTGACATGTTTAATGAACATGAACTTCAG

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|20811283|gb|BQ295761.1|BQ295761
EST:     ATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAG                         ATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCA
genomic: ATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAGgtaaaaagat ... tctatcatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCA
EST: gi|6020745|gb|AW065553.1|AW065553
EST:     ATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAG                         ATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCA
genomic: ATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAGgtaaaaagat ... tctatcatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCA
EST: gi|26456975|gb|CA828558.1|CA828558
EST:     ATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAG                         ATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCA
genomic: ATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAGgtaaaaagat ... tctatcatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 36

TGAAGAAGAACTTCTCCCTGGTGGGAGGGACATGCGTGTTACGAATGATAATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAGgtaaaaagat ... tctatcatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCAAAAGACTGGATTGATATGTTCAATGAACATGAAATTCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 30

TGAAGAAGAACTTCTCCCTGGTGGGAGGGACATGCGTGTTACGAATGATAATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAGgtaaaaagat ... tctatcatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCAAAAGACTGGATTGATATGTTCAATGAACATGAAATTCAG


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

TGAAGAAGAACTTCTCCCTGGTGGGAGGGACATGCGTGTTACGAATGATAATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAGgtaaaaagat ... tctatcatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCAAAAGACTGGATTGATATGTTCAATGAACATGAAATTCAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 41

TGAAGAAGAACTTCTCCCTGGTGGGAGGGACATGCGTGTTACGAATGATAATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAGgtaaaaagat ... tctatcatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCAAAAGACTGGATTGATATGTTCAATGAACATGAAATTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatttggatgcattggaaggctttgctaattgttttcctggtttctatcatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCAAAAGACTGGATTGATATGTTCAATGAACATGAAATTCAG
                         tgctaat  putative branch site (score: 41)
                                  ttttcctggtttct  putative PPT
                            taattgtttt  TA-rich tract