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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaacacccaatatcatttcataggagctaattggacaaaatttgcactagcacatttttcttttcttgtgtggatttgaagtttatagtggatatttgacaacctgaactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAAGGTGACTATGACACATTTGAGAGGACAAGGGAAGAGCACCTTAAGAATC

Basic information

species Zea mays
transcript GRMZM2G013890_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 7
----------------gtatgaacacccaatatcatttcataggagctaattg-gacaaa---------atttgcac-tagcacatttttcttttcttgtgtggatttgaagtttatagtggatatt--tgacaacctgaactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAAGGTGACTATGACACATTTGAGAGGACAAGGGAAGAGCACCTTAAGAATC
                 ||||| ||    |||| ||     |||||||||||  |||| |         |||   |  ||| | ||||   | | | | | |    |||   | || |     || |  ||| | |   || || |||||| |||||||| || ||||||||||||||   ||| |||||||||||||||||||| ||||||||||| |||||||||||||| |||||||||||||| |
gtatgcagtatgatgattatgatcatgtcatattatcatgaaggagctaattttgacagagcgtccttaattcatatgtagtatatttgcatgtgcatttttttccttgtcatgtaaatcacttaatgctgatagcaataaattcttagGTCGTCACCGACATTCTTCATCTGCATGGACAAAAGCTACATGCTTACAAAGGTGATTATGACACATTCGAGAGGACAAGGGAGGAGCACCTTAAGAACC
















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|33094472|gb|CF054466.1|CF054466
EST:     GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACG                         GTCGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA
genomic: GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacac ... aactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA
EST: gi|60343993|gb|DN210966.1|DN210966
EST:     GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACG                         GTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA
genomic: GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacac ... aactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA
EST: gi|211238345|gb|FL044423.1|FL044423
EST:     GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACG                         GTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA
genomic: GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacac ... aactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA
EST: gi|20301286|gb|BQ164229.1|BQ164229
EST:     GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACG                         GTTGTCACCGATATCCTTCATCTGCATGGTAGAAAAC
genomic: GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacac ... aactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAAC
EST: gi|60349362|gb|DN216335.1|DN216335
EST:     GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACG                         GTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA
genomic: GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacac ... aactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA
EST: gi|71307303|gb|DR789832.1|DR789832
EST:     GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACG                         GTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA
genomic: GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacac ... aactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA

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), 46 (downstream exon)
Score: 136

CCATCTTGATCTTCATGCTGTGTTATGGCTAGAAACTTATCTCCTGAAGTGGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacac ... aactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAAGGTGACTATGACACATTTGAGAGGACAAGGGAAGAGCACCTTAAGAATC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 139

CCATCTTGATCTTCATGCTGTGTTATGGCTAGAAACTTATCTCCTGAAGTGGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacac ... aactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAAGGTGACTATGACACATTTGAGAGGACAAGGGAAGAGCACCTTAAGAATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

CCATCTTGATCTTCATGCTGTGTTATGGCTAGAAACTTATCTCCTGAAGTGGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacac ... aactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAAGGTGACTATGACACATTTGAGAGGACAAGGGAAGAGCACCTTAAGAATC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 84

CCATCTTGATCTTCATGCTGTGTTATGGCTAGAAACTTATCTCCTGAAGTGGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacac ... aactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAAGGTGACTATGACACATTTGAGAGGACAAGGGAAGAGCACCTTAAGAATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttgtgtggatttgaagtttatagtggatatttgacaacctgaactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAAGGTGACTATGACACATTTGAGAGGACAAGGGAAGAGCACCTTAAGAATC
                                atttgac  putative branch site (score: 84)
                                               cttttt  putative PPT
            atttgaagtttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaacacccaatatcatttcataggagctaattggacaaaatttgcactagcacatttttcttttcttgtgtggatttgaagtttatagtggatatttgacaacctgaactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAAGGTGACTATGACACATTTGAGAGGACAAGGGAAGAGCACCTTAAGAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA