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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCGTGGGCGTGGATTTGGAGGCCGTGGTGGAAGGGGTGACAGAGGCCGTGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaattgcttgttttaagttttgttttgccagattaattttgtatccagtttgagctatgtttgttgtgtccgcccttgatttggaaccttgccttgaattttgtag

Basic information

species Zea mays
transcript GRMZM2G001850_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G001850_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os04g52960.1 (Oryza sativa), 5'ss of exon 19
AGCCGTGGGCGTGGATTTGGAGGCCGTGGTGGAAGGGGTGACAGAGGCCGTGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaattgcttgttttaagttttgttttgccagattaattttgtatccagtttgagct--atgtttgttgtgtccgcccttgat--ttggaacc--ttgccttgaattttgtag
 || |||  ||||||  |||  |  |   ||| ||||||||||| |||| ||||||| ||||||| || ||||  |||| |||||||||| ||||| ||||||||   |     |    || ||    ||| ||    |  ||       | | |||  ||  ||||  | |  ||    |  | ||  ||   ||   |||| ||    | || ||
CGCGGTGACCGTGGACGTGGTAGAGGCTTTGGTAGGGGTGACAGGGGCCATGGTGGACGGGGTACACCGTTCAAGCAGAGCGCTGGTACACCTAGTGCAGgtaaaacttctaccgcaccaaattgcaatttacccagctt-ttacactcgctgcttggacttgatgtaggataagtggagctgtcataattaatactatttgctttcttatctgcag
















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|60352099|gb|DN219072.1|DN219072
EST:     TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
EST: gi|211390614|gb|FL418023.1|FL418023
EST:     TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGACCACCTTTGGTGATGACGA
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGA
EST: gi|78076793|gb|DV505227.1|DV505227
EST:     TGGTGGAAGGGGTACGCCTTTCTGACAGACCGCTGGTACAGCTAGTTCCG                         GAAAGAAGACCACCTTCGGTGATGACGATTGAAGATCCATGGCTGGCTATT
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
EST: gi|71327897|gb|DR800580.1|DR800580
EST:     TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
EST: gi|71320522|gb|DR797006.1|DR797006
EST:     TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
EST: gi|166532536|gb|EG115693.1|EG115693
EST:     TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCA
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCA
EST: gi|166556412|gb|EG107522.1|EG107522
EST:     TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCA
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCA
EST: gi|37386475|gb|CF630423.1|CF630423
EST:     TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
EST: gi|60355101|gb|DN222074.1|DN222074
EST:     TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
EST: gi|78076792|gb|DV505226.1|DV505226
EST:     TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
EST: gi|32936352|gb|CF041171.1|CF041171
EST:     TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
EST: gi|113632791|gb|DW790443.1|DW790443
EST:     GGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAAG                         GAAAGAAGACCACCTTTGGTGATGACGAATTGAAGATCCA
genomic: GGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACA-Ggtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGA-TTGAAGATCCA
EST: gi|166429741|gb|EG165573.1|EG165573
EST:     GTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGAACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTAT
genomic: GTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGA-CCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTAT
EST: gi|26557920|gb|CA830155.1|CA830155
EST:     TGGCGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
EST: gi|149045940|gb|EE047938.2|EE047938
EST:     TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGACCCCCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
EST: gi|61118397|gb|DN559358.1|DN559358
EST:     TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
EST: gi|166470174|gb|EG125534.1|EG125534
EST:     TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCA
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCA
EST: gi|211355109|gb|FL475414.1|FL475414
EST:     TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
EST: gi|166614887|gb|EG290546.1|EG290546
EST:     GGTGGAAGGGGTACGCCTTTCAGACAGACCGACTGGTACAGCTAGTACAG                         GAAAGA-GACCACCTT
genomic: GGTGGAAGGGGTACGCCTTTCAGACAGACCG-CTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTT
EST: gi|211324531|gb|FL445883.1|FL445883
EST:     TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
EST: gi|6021892|gb|AW066820.1|AW066820
EST:     TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGACCACCTTTGGTGATGACGATTGAAGATNCCATGGCTGGCTAT
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGAT-CCATGGCTGGCTAT
EST: gi|60400636|gb|DN233443.1|DN233443
EST:     TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
EST: gi|110480718|gb|EE010818.1|EE010818
EST:     TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAG                         GAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT
genomic: TGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATT

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), 30 (downstream exon)
Score: 223

AGCCGTGGGCGTGGATTTGGAGGCCGTGGTGGAAGGGGTGACAGAGGCCGTGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATTATAGTGAAAAACGCAAACTATATTGTACCGTTCAGACCTATTGTTATCT


Block sizes: 49 (upstream exon), 30 (downstream exon)
Score: 84

AGCCGTGGGCGTGGATTTGGAGGCCGTGGTGGAAGGGGTGACAGAGGCCGTGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATTATAGTGAAAAACGCAAACTATATTGTACCGTTCAGACCTATTGTTATCT


Block sizes: 49 (upstream exon), 30 (downstream exon)
Score: 135

AGCCGTGGGCGTGGATTTGGAGGCCGTGGTGGAAGGGGTGACAGAGGCCGTGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATTATAGTGAAAAACGCAAACTATATTGTACCGTTCAGACCTATTGTTATCT


Block sizes: 48 (upstream exon), 30 (downstream exon)
Score: 85

AGCCGTGGGCGTGGATTTGGAGGCCGTGGTGGAAGGGGTGACAGAGGCCGTGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaatt ... aattttgtagGAAAGAAGACCACCTTTGGTGATGACGATTGAAGATCCATGGCTGGCTATTATAGTGAAAAACGCAAACTATATTGTACCGTTCAGACCTATTGTTATCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCGTGGGCGTGGATTTGGAGGCCGTGGTGGAAGGGGTGACAGAGGCCGTGGTGGAAGGGGTACGCCTTTCAGACAGACCGCTGGTACAGCTAGTACAGgtaaacaattgcttgttttaagttttgttttgccagattaattttgtatccagtttgagctatgtttgttgtgtccgcccttgatttggaaccttgccttgaattttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG