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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctattggtctttgtgcgatgcctccatggactgtggactgggaattaactatgctgttcatggaaactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACCCGACTTCGATGCTGCTGTGAAGTTAGGATCGATGACCTAACACAATTCT

Basic information

species Zea mays
transcript GRMZM2G161969_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161969_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os07g22720.2 (Oryza sativa), 3'ss of exon 18
--gtaagctattggtctt-------tgtgcgatgcctccatggactgtggactgggaattaactatgctgttcatggaaactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACCCGACTTCGATGCTGCTGTGAAGTTAGGATCGATGACCTAACACAATTCT----
   ||  || | | ||||       |    |||| || ||||||   ||| |  | |||||||| |  |  |  ||       |  |||||||||||| || |||||||||||||||||||||||||| |||||||| || || || ||| | |||||||| ||     ||| | | || || |||||    
gtatactctttagatcttatcggaataaatgatggcttcatggatcatgggcaagaaattaacttttgttcttgtgcgcttactctagGTGCAATCGGGGCAGAATTTCTGAAAGCATTCAAGGGCTATATCGAGAATCCAACCTCAATGTTACTGTGAAGCTAAA---GATCATCAAA-ACTATTCTTCCC

upper sequence: GRMZM2G161969_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 3'ss of exon 18
--------gtaagctattggtctttgtgcgatgcctccatggactgtggactgggaattaactatgctgttcatggaaactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACCCGACTTCGATGCTGCTGTGAAGTTAG-GATCGATGACCTAACACAATTCT
         |||||  |   |   |    |||   || | ||||  | | || | || ||||| || |  |  ||     | |  |||||| ||||| || |||||||||||||||||||||||||| |||||||| || |  || ||| | |||||||||||  ||||    |    |  |   || 
gtatactcttaagccttatctgaatacatgatagttctacggaccataggctagaaaataactttgttcat-gtgtgctttctctagGTGCTATCGGCGCAGAATTTCTGAAAGCATTCAAGGGCTATATCGAGAATCCAAACTCAATGTTACTGTGAAGTTAAAGATCAGCAAAACTATTCTTCTC-

upper sequence: GRMZM2G161969_T01 (Zea mays), 3'ss of exon 14
lower sequence: AT3G13930.1 (Arabidopsis thaliana), 3'ss of exon 19
gtaagctattggtctttgtgcgatgcctccatggactgtggactgggaattaactatgctgttcatggaaact----gtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACCCGACTTCGATGCTGCTGTGAAGTTAGGATCGATG-ACCTAACACAATTCT
|||    ||  | || |      |     |||      |   |     ||  |  | |      | |  | ||    ||||||||||||| || || || |  |||||||||||||||||||||||||||| |||    || ||| |||| | || ||  ||   |   ||  | || ||    
gtacagaatccgcctctcattcctattgtcattattaatcatcacctcatcgaaaacgtctaataagtcatcttcctgtgcagGTGCAATTGGAGCCGAGTGGCTGAAAGCATTCAAGGGCTACATCGAGACCCCAGAATCTATGTTGCTCTAAAATTCAGACGCACACACACATCAAAAGCT-

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|20301579|gb|BQ164522.1|BQ164522
EST:     TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG                         GTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
genomic: TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
EST: gi|20336914|gb|BQ172544.1|BQ172544
EST:     TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG                         GTGCAATCGGTGCGGAATTTCTGAGAGCATTCAAGGGCTACATCGAGAACC
genomic: TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
EST: gi|71329666|gb|DR801555.1|DR801555
EST:     TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG                         GTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
genomic: TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
EST: gi|21809699|gb|BQ668017.1|BQ668017
EST:     TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG                         GTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
genomic: TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
EST: gi|5439400|gb|AI820321.1|AI820321
EST:     TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG                         GTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
genomic: TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
EST: gi|20208397|gb|BQ134486.1|BQ134486
EST:     TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG                         GTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
genomic: TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
EST: gi|5343148|gb|AI795333.1|AI795333
EST:     TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG                         GTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
genomic: TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
EST: gi|148935652|gb|EC879696.2|EC879696
EST:     TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG                         GTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
genomic: TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
EST: gi|4776441|gb|AI665444.1|AI665444
EST:     TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG                         GTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
genomic: TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC

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: 112

TGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACCCGACTTCGATGCTGCTGTGAAGTTAGGATCGATGACCTAACACAATTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

TGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACCCGACTTCGATGCTGCTGTGAAGTTAGGATCGATGACCTAACACAATTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

TGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACCCGACTTCGATGCTGCTGTGAAGTTAGGATCGATGACCTAACACAATTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 158

TGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACCCGACTTCGATGCTGCTGTGAAGTTAGGATCGATGACCTAACACAATTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctccatggactgtggactgggaattaactatgctgttcatggaaactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACCCGACTTCGATGCTGCTGTGAAGTTAGGATCGATGACCTAACACAATTCT
                       aattaac  putative branch site (score: 158)
                       aattaactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctattggtctttgtgcgatgcctccatggactgtggactgggaattaactatgctgttcatggaaactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACCCGACTTCGATGCTGCTGTGAAGTTAGGATCGATGACCTAACACAATTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT