Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaatatgctaagcaacaccaattgcactgcaaattaccatttgattctttacatgttaaccacaatggctcactgggaaggatggaaatttgtgtgtagGTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAAC

Basic information

species Zea mays
transcript GRMZM2G073774_T01
intron # 7
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 7
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 7
acaatatgctaagcaacaccaattgcactgcaa-attaccatttg-attctttacatgttaaccacaatggctcactgggaaggatggaaatttgtgtgtagGTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAAC
||    || |    |    ||  || | |       ||| ||    ||  |||  || ||  ||| ||||||| |   |||||     |||| ||  | ||||| || |||||||||||||| |||||| |||| |||||||| ||||| |||||||||||||| 
acttattgttgtttagt-tcatctgtagtaagttgatactataaacatagtttttat-ttctccataatggcttatgtggaagatctaaaatgtggctctagGTGGATGCAGCCCTTATAGCCACAGGACGGGCACCATTCACAAAAGGACTTGGCTTGGAAAAT
















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:     TCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAG                         GTTGACGCAGCCCTTATAGCTACAG
genomic: TCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAGgtaacatttc ... ttgtgtgtagGTTGACGCAGCCCTTATAGCTACAG
EST: gi|67016819|gb|CO445568.1|CO445568
EST:     TCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAG                         GTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTT
genomic: TCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAGgtaacatttc ... ttgtgtgtagGTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTT
EST: gi|6536537|gb|AW224850.1|AW224850
EST:     TCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAG                         GTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTT
genomic: TCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAGgtaacatttc ... ttgtgtgtagGTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTT
EST: gi|31354606|gb|CD438963.1|CD438963
EST:     TCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAG                         GTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTT
genomic: TCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAGgtaacatttc ... ttgtgtgtagGTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTT
EST: gi|6626525|gb|AW258057.1|AW258057
EST:     TCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAG                         GTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTT
genomic: TCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAGgtaacatttc ... ttgtgtgtagGTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTT
EST: gi|32932110|gb|CF036922.1|CF036922
EST:     TCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAG                         GTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTT
genomic: TCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAGgtaacatttc ... ttgtgtgtagGTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTT
EST: gi|31353176|gb|CD437533.1|CD437533
EST:     TCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAG                         GTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTT
genomic: TCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAGgtaacatttc ... ttgtgtgtagGTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTT

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: 122

ATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAGgtaacatttc ... ttgtgtgtagGTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAAC


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 63

ATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAGgtaacatttc ... ttgtgtgtagGTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAAC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 59

ATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAGgtaacatttc ... ttgtgtgtagGTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAAC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 125

ATTACTCCTGCAAAGGATGGAAAACCTGTGCTCATCGAGCTTATTGATGCAAAGACAAAGGAGCACAAAGAAACCCTTGAGgtaacatttc ... ttgtgtgtagGTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttacatgttaaccacaatggctcactgggaaggatggaaatttgtgtgtagGTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAAC
                                         aaatttgt  TA-rich tract