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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatctccttgcaccatcgatcgcattgatgagtctagtctcaaacaaatcccatgtttccag

Basic information

species Zea mays
transcript GRMZM2G088245_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088245_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os10g33640.1 (Oryza sativa), 5'ss of exon 6
GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatctcct---tgcaccatcgatcgcattgatgagtctagtct----caaacaaatcccatgtttccag--------
|| ||||| || ||||| ||||| |||||||| ||||||||||||||||| || || || || || ||||| ||||| ||||||||||| | | | | ||| || | ||| | ||| |||| || || ||
GCATACTCCACTGTCGGTACACCGGACTACATTGCTCCAGAAGTTCTTCTAAAAAAGGGTTATGGAATGGAGTGTGATTGgtaagcatcgtttacataaatatctcgtgccatggacctcttgagtttgcagtaaagaaattgaataatttcaactatctag

upper sequence: GRMZM2G088245_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA13G18670.2 (Glycine max), 5'ss of exon 6
GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatc-tccttgcaccatcgatcgcattgatgagtctag-----tctcaaacaaatcccatgtttccag---------------------------
||||| || || || || |||||||| || || ||||||||||||||| |||||||||| || |||||||||||||| |||| || | | | || | || | | | | ||| || ||||| |
GCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTGgtgagttttatgcatgtgaatgttggcatgttatcaaatattggtttctctttgccatggtgcatgtatatcatagcatccaagtttcaccaagttgttg

upper sequence: GRMZM2G088245_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA10G04410.2 (Glycine max), 5'ss of exon 7
GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatc-tccttgcaccatcgatcgcattgatgagtctagtctcaaacaaatcccatgtttccag--------------------------------
||||| || || || || |||||||| || || ||||||||||||||| |||||||||| || |||||||||||||| |||| || | | | || | || | | | | | ||||| |
GCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTGgtgagttttatgcatgtgaatgttggcatgttatcaaatattggtttctctgctatttgtgtttgtatatcatagcatccaagtttatcttttaattcat

upper sequence: GRMZM2G088245_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA20G35110.1 (Glycine max), 5'ss of exon 6
GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatctccttgcaccatcga--tcgcattgatgagtctagtctcaaacaaatcccatgtttccag--------------------------------------------------
|| || || || ||||||||||| ||||| || || || |||||||||||||||||||| || || ||||||||||| ||||| |||| | || | | | || | || | || | |||| |
GCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTGgtat-tatctaatgtgtttttctacttttccttttcaaaaataccttgaagttccctttgtttttctaaacttcatattatttcaatatgttctgatgagattgtggtaatgtttccag

upper sequence: GRMZM2G088245_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA10G00830.1 (Glycine max), 5'ss of exon 6
GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaag---------------catctccttgcaccatcgatcgc---attgatgagtctagtctcaaacaaatcccatgtttccag-----------------------------
|| || || || || |||||||| || || || |||||||||||||||||||||||||| || || |||||||||| |||||| || | || || || | || | || | | | ||| ||||||| |
GCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTGgtaatatagaatgtgttttctatttttctgtttcaaaagtctccccatggccacccctccccccttataaacttaatgtttcaatgcattctgatgttgtgtcaatgcttccag

upper sequence: GRMZM2G088245_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA19G34920.1 (Glycine max), 5'ss of exon 6
GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatc-tccttgcaccatcgatcgcattga--tgagtctagtctcaaacaaatcccatgtttccag--------------------------------
|| || || || || || ||||| || || || |||||||||||||| |||| ||||| || |||||||||||||| |||| || | | |||| | | ||| |||| | | | | | | | | ||||| |
GCGTATTCTACGGTTGGTACACCGGATTATATTGCTCCAGAAGTTCTAATGAAAAAAGGTTATGGGATGGAATGTGATTGgtgagttttgtgcttgta--aatgataacattaaatttattttcactttgctctttggtcctgtttggatgaaaagctataaaatcttttgattttttacat

upper sequence: GRMZM2G088245_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA10G32480.1 (Glycine max), 5'ss of exon 6
GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatctccttgcaccatcga--tcgcattgatgagtctagtctcaaacaaatcccatgtttccag--------------------------------------------------
|| || || || ||||||||||| ||||| || || || |||||||||||||||||||| || || ||||||||||| ||||| |||| | || | | | || | || | || | ||| |
GCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTGgtat-tatctaatgtgtttttctagttttccttttcaaaaataccatgaagttccctttgtttttgtaaacttcatattatttcaatatgttctgatgagattttggtaatgtttccag

upper sequence: GRMZM2G088245_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA02G00580.2 (Glycine max), 5'ss of exon 7
GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaa----gcatctccttgcaccatcgatcgcattgatgagtctagtctcaaacaaatcccatgtttccag---------------------------------------------------------------------
|| || || || || |||||||| || || || |||||||||||||||||||||||||| || || |||||||||| |||||| | || | || | | || || | ||||| | | ||| | ||
GCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTGgtaatatagaatatgtttt--ctacttttctttttcaaaagtctccctaagggccaccccccttcccccttttaaacttattgtgtcaatgcattctgatgttgtgtcaatgcattctaatgttgtgtcaatgcttccag

upper sequence: GRMZM2G088245_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT1G03920.1 (Arabidopsis thaliana), 5'ss of exon 5
GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatctccttgcaccatcgatcgcattgatgagtctagtctcaaa--caaatccc----atgtttccag------------
|||||||| ||||| || |||||||||||||| || || ||||| | | |||||||| ||||| ||||||||||||||||| | | | | || ||| | | | ||| || ||| |||||| |
GCTTACTCAACCGTTGGTACACCAGACTACATTGCACCTGAAGTCTTGTTAAAGAAAGGATACGGCATGGAATGTGACTGgtacgtgtacacacttgtctattttcaacttgttaacaaagaacaaaaaagtaagtccttagaatgtttttaaaaaatcctccag

upper sequence: GRMZM2G088245_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT2G20470.1 (Arabidopsis thaliana), 5'ss of exon 6
GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatct-------ccttgcaccatcgatcgcattgatgagtctagtctcaaacaa---atcccatgtttccag-----------------------
||||| || || || || |||||||| ||||| |||||||||||||| ||||||||||||| |||||||| ||||||||||||||| | || || | || | | | | | | | ||| || |||
GCTTATTCCACAGTTGGCACACCAGATTACATAGCTCCAGAAGTTCTGTTGAAGAAAGGCTATGGGATGGAGTGTGACTGgtaagcacttgagactcttttttgtttgtgacagtatcacaggctatgagcatacatactccatcatatatttttgtgtttagccaatttcaaaagaaga

upper sequence: GRMZM2G088245_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv07s0005g03690.t01 (Vitis vinifera), 5'ss of exon 6
GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatctcc-----ttgcacc--atcgatcgcattgatgagtct---agtctcaaacaaatcccatgtttccag-----------------------
||||| || || || || ||||||||||| ||||||||||||||| | |||||||||| || |||||||||||||| ||||||| | | | | | || | || | ||| | | | | ||| ||| ||||||
GCTTATTCTACTGTTGGGACACCAGACTATATCGCTCCAGAAGTTTTATTGAAGAAAGGTTATGGGATGGAATGTGATTGgtaagtggtttacacaatgggaactgattggtcatttggatatcccatggaatttgaaattgttccgatgtttttcctttacatagcatttgaaatgatt

upper sequence: GRMZM2G088245_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 5'ss of exon 6
GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaag--------------catctccttgcaccatcgat----cgcattgatgagtctagtctcaaacaaatccc-----atgtttccag
|| || || || || || || || |||||||| ||||||||||| || || |||||||| || |||||||| ||||| |||| | |||| ||| | ||| | | ||| ||| ||| | || | | ||| || | |||||
GCCTATTCTACTGTTGGTACCCCTGACTACATTGCTCCAGAAGTGCTGCTTAAGAAAGGATATGGGATGGAGTGTGATTGgttggttctctaaaactgtcatcatcttctatgatctgttttccccatggattagtttcctcatataaccatctgtttgaatttctccag

upper sequence: GRMZM2G088245_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 5'ss of exon 6
GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatctccttg-----caccatcga---tcgca-ttgatgagtctagtctcaaacaaatcccatgtttccag------------------------
|| || || || ||||| || ||||| || || ||||| ||||| || |||||||||||||| |||||||| ||||||||||| ||||| ||| | | || | || |||||| || |||| | | |
GCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTGgtatgcatcgaattgattcatattactgaaacttgctcttgatgtccctggtctaagttgagctgtgccccatatgacattgactcattatttggagttg

upper sequence: GRMZM2G088245_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S22_429V6.1 (Physcomitrella patens), 5'ss of exon 6
GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatctccttgcaccatcgatcgcattgatgagt---ctagtctcaaacaaatcccatgtttccag--------------------------
|| || ||||| ||||| || |||||||| |||||||| ||||| || ||||||| || || |||||||| ||||||||||| | | | ||| | | | | ||| | |||| | | | | | ||||| |
GCGTATTCGACAGTCGGCACTCCAGACTATATCGCTCCGGAAGTACTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTGgtatgtagcaagttgtgctccttggcccctgaatgcatttcctagcttttta-agttgttttttttccggaggtttgaacgtaagtttctctgcag

upper sequence: GRMZM2G088245_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 5'ss of exon 6
GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatctccttgcaccatcga---tcgcattgatgagtctagtctcaaacaaatcccatgtttccag-------------------------------------------------
|| || || || ||||| || ||||||||||||||||| ||||| || ||||||| || || |||||||| ||||||||||| | | | | | || | | | | | || | |||| | | | |
GCCTATTCAACAGTCGGCACTCCAGACTACATCGCTCCTGAAGTCCTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTGgtatgtgacaagtcgttctcctgaatctttctctttttatccttggctcatgatgtacttgcttagcttgataaagttcttgttgtgttcaaaaaggttgaacgtaagttttcctacag

upper sequence: GRMZM2G088245_T01 (Zea mays), 5'ss of exon 6
lower sequence: EFJ29515 (Selaginella moellendorffii), 5'ss of exon 6
GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatctccttgcaccatcgatcgcattgatgagtctagtctcaaacaaatcccatgtttccag
||||| || || ||||| || ||||| || || ||||| |||||||| |||||||| || ||||||||||| ||||| ||||||| | | || || || | | | | || || | ||
GCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTGgtaagaggcatttc---tgattgaaaatatctaccggcttgatt-------gatttatggtgcctag

upper sequence: GRMZM2G088245_T01 (Zea mays), 5'ss of exon 6
lower sequence: EFJ28086 (Selaginella moellendorffii), 5'ss of exon 6
GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatctccttgcaccatcgatcgcattgatgagtctagtctcaaacaaatcccatgtttccag
||||| || || ||||| || ||||| || || ||||| |||||||| |||||||| || ||||||||||| ||||| ||||||| | | | || || || | | | | || || | ||
GCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTGgtaagaggcacttc---tgattgaaaatatctaccggcttgatt-------gatttatggtgcctag

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|71298682|gb|DR785316.1|DR785316
EST:     ATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG                         GTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATT
genomic: ATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatct ... atgtttccagGTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATT




















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 1 RNA-Seqlibrary.


Block sizes: 44 (upstream exon), 13 (downstream exon)
Score: 4

GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatct ... atgtttccagGTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATTCTATTCTGACGAGCCTATGACTACTTGCCGAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatctccttgcaccatcgatcgcattgatgagtctagtctcaaacaaatcccatgtttccag

- - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA