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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgatctcaccatgcgatggaaacttcatattctttctgttaagtaaaactgatcttgaatttatgcatgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA

Basic information

species Zea mays
transcript GRMZM2G423861_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 9
gtctgat--ctcaccatgcgatggaaacttcatattctttctgttaagtaaaactgatcttgaatttatgcatgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
||||||| || |||| | || ||| ||| |||||| | | | || || | ||| ||| | |||||||||||| ||||||||||| |||||||||||||||||||||||||||||| | ||||| |||||||||||||| ||||||||||| ||||||||||||||||
gtctgatgcctaaccacatgttg-aaatgctatacgttttctgccagttttagctaatttctt-tttctgcgttaatgcagGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAA

upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 11
---------gtctgatctca-ccatgcgatgg-aaacttcatattctttctgttaagtaaaactgatctt------gaat---ttatgcatgaatg-----cagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
|||| | | | ||| || || | | | | | | | || || || ||| |||| || | || ||| ||||| || ||||||||||| ||||| ||||||||| | || ||||| ||||| |||||||| ||||||||||| |||||||||||||| || || |||||||
gtaagactaacatgatttaaattttaagattataaggtttaaaatttctttttaaaaacgaattgtgcttttaattgaatgtttttttaataaattattcccagGTCCATTTTTTCCGTCCCGTTCCAAAGGAATATATGCACTCTGCTGAATTGAGAGACATAATGCAATTTGGAAGCAGCAATACTGCAGTATTTTTTAAAA

upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 14
--------------------gtctgatctcaccatgcgatggaaacttca-tattctttctgttaagtaa--aactgatcttgaatttatgcat--------------gaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
|| | || | | | | | || | |||| | |||| || ||||| ||| | || || | | | || |||| ||||||||||||||||| ||||||||| | || || || || || |||||||| ||||||||||| |||||||||||||| || || |||||||
gtatgactaaacaaaaaaataactagttaaactaaacattatatagtttactattacaattattaaaaaatgaactgtgcttttaattgtgttttttcttgatcaattggctatagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGCAATACTGCAGTCTTTTTTAAAA

upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 11
----------------gtctgatctcaccatgcgatggaaacttcat-attctttctgttaagtaa--aactgatcttgaatttatgca----------------tgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
|| | || | | | | | || || ||| | |||| || || || ||| | || || || | || |||| ||||||||||||||||| ||||||||| | || || || || || |||||||| ||||||||||| ||||| |||||||| || ||||||||||
gtatgactaaatgaaaaactagttaaactaaacattatatagtttatcattacaattattaaagaatgaattgtgcttttaattgtgtgccttttcttgatccattggctatagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGTAATACTGCAGTCTTCTTTAAAA

upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 11
---------gtctgatctcaccatg-cgatggaaacttcatattctttctgttaagtaaaactgatcttgaatttatgc---atgaatg-----cagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
|||| | | | | || || | | | | | | || || || |||||||| | || ||| ||||| || ||||||||||| |||| ||||||||| | || ||||| || || || ||||| ||||||||||| |||||||||||||| || || |||||||
gtaatactaacatgattaaattttaacactataaggtttaaaacttctttttaaaaactaattg--tttgaattttttttcaataaattattcccagGTCCATTTTTTCCGTCCCATTCCAAAGGAATATATGCACTCTGCTGAGTTGAGGGACATAATGCAATTTGGAAGCAGCAATACTGCAGTATTTTTTAAAA

upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 8
------------------gtctgatctcaccatgcgatggaaact-tcatattctttctg---ttaagtaaa----actgatcttgaatttat-----gcatgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
|| | | | | | ||||| | || | || | | || | | || |||||||| | || | || ||||||||||||| || || ||||| || |||||||| || ||||| ||| || | ||||||||||||||||| ||||| || |||||||| || || ||||
gttagtctcaatataaatgttatacattatgactttaaaaaaactgttattgttgtttggaattcaaatctatgttgttggatttgaatttgttgtttgctttcttgtagGTTCACTTTTTTCGACCGGTTCCTAAAGAATATCTGCACTCTGCTGAACTACGTGACATCATGCAATTTGGCAGCAGTAACACTGCTGTCTTTTTCAAAA

upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 10
-------------------gtctgatctcaccatgcgatggaaacttcatattc----tttctgttaagtaaaactgatcttgaattta----tgcatgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
| | || | | | | || ||| || || || | | | | | ||| || | ||||||| | ||| |||||||| ||||||||||||||||| || || ||| | |||||||| ||| ||||||| || ||||||||||||||||||||||||||||| || ||||| |
gtgagtcagagttatattattataatgtatctgtacattgcaaatttgatgtttgaattatagatctattgcaacagaacatgaatttgattgttcattctcacagGTTCATTTTTTCCGTCCAGTTCCAAAAGAGTATTTGCATTCTGCTGAACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGA

upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ30174 (Selaginella moellendorffii), 3'ss of exon 10
gtctgatctcaccatgcgatggaaacttcatattctttctgttaagtaaaactgatcttgaatttatgcatgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
| | | | | ||||| ||| | | || | | || ||| | | |||||||| |||||||| ||||| || || |||||| | ||||| || || | |||||||||||||||||||| || |||||||| || || || |||||||
-----------gtacgtgcaagtatattcatgttcgctgttttga-----------catgtgtttcttaa------cagGTTCATTTTTTCCGGCCAGTACCTAAAGAATATTTACATTCGGCTGAGCTGAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAA

upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ06058 (Selaginella moellendorffii), 3'ss of exon 10
gtctgatctcaccatgcgatggaaacttcatattctttctgttaagtaaaactgatcttgaatttatgcatgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
| | | | | | || | | |||| | || | |||||||| |||||||| ||||| || || |||||| | ||||| || || | |||||||||||||||||||| || |||||||| || || || |||||||
-------------------------gtacgtgcaagtatattcatgttcg--cggttttga-catgtgtttcttaacagGTTCATTTTTTCCGGCCAGTACCTAAAGAATATTTACATTCGGCTGAGCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAA

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|18383721|gb|BM416921.1|BM416921
EST:     GCTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGG                         G-TCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTA
genomic: GCTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGGgtctgatctc ... atgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTA
EST: gi|18649769|gb|BM498588.1|BM498588
EST:     CTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGG                         GTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTA
genomic: CTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGGgtctgatctc ... atgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTA

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: 273

TCTTCCATATGGGAACTCTGTTTTCTTTAGTGTCCGTAAGATTGATGATCCAATAGGATTGCTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGGgtctgatctc ... atgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 40

TCTTCCATATGGGAACTCTGTTTTCTTTAGTGTCCGTAAGATTGATGATCCAATAGGATTGCTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGGgtctgatctc ... atgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 43

TCTTCCATATGGGAACTCTGTTTTCTTTAGTGTCCGTAAGATTGATGATCCAATAGGATTGCTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGGgtctgatctc ... atgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 117

TCTTCCATATGGGAACTCTGTTTTCTTTAGTGTCCGTAAGATTGATGATCCAATAGGATTGCTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGGgtctgatctc ... atgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttcatattctttctgttaagtaaaactgatcttgaatttatgcatgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
                         aactgat  putative branch site (score: 117)
 ttaagtaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgatctcaccatgcgatggaaacttcatattctttctgttaagtaaaactgatcttgaatttatgcatgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT