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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA

Basic information

species Zea mays
transcript GRMZM2G330298_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
gtatgcta-aatctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
||| | | ||||||||||| |||||| ||| | | |||||| || || | | ||| || | | || ||| || || | | |||||||| ||||||||||||| ||||||||||| ||||||||||||||||||||||| |||||||| ||||| || || |||||||||||||| || ||||||
gtaagttttgatctgaaattattatctt-actacct-gtagttggtt-aacatcctcaccttaaa----aagattatg---aactctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA

upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G16380.1 (Glycine max), 3'ss of exon 9
----gtatgctaaatctgaaattactatctttacttcttcatagttgatt--caataccatcaactca-tattacaaaattctggtcaatttctct-tagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
|| || || | || ||| | ||||||| || || ||| | | | | | | ||| | || | | ||| ||| | || || || |||||||||||||| |||||||| || |||||||||||||||||||| ||||||||||||||||||||| | || || || |||
attgcaatattaccacttggtcgaaacctattttttccagctggttgattttcactatcatgcatttgctgacatatatatcttttgaaaattgatgtagTTATGTGGCGCCGGAGTATGCAATGACTGGGCATCTTCTTGTTAAGAGTGATGTTTACAGCTATGGTGTTGTTCTTCTTGAGCTTTTGACTGGAAGAAAA

upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G02800.1 (Glycine max), 3'ss of exon 8
-------------------------------------------------------------------------------------------------gtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtca-atttctctt-------agGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
| | | | | | | | | | | ||| ||| | | | | || | | | | || | ||| ||||| || || | |||||||||||||||||||| ||||||||||| || || ||||||||||||||||| || ||||| || |||||||| || || || || ||
gtaacaatcccttcctagcccttttatgttgatgcttttatggatcatagacgtgatggccaaatgaacacgtttacaaagtactcatttcattccagcttcttgtgtttatcagacttttatgcggatatacattaccatttctgtgcatttcgtctagatgaaactgattttgtgacattgctcttgttttgcagCTACGTAGCTCCTGAATATGCAATGACCGGCCATCTTCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG

upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G07140.1 (Glycine max), 3'ss of exon 9
-----gtatgctaaatct-gaaattactat----ctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
||| | | | ||| || | | |||| | || | || ||| | | || | ||||| || | | || | | | || ||| | ||||| || ||||||||||| || |||||||| || |||||||||||||||||||| |||||||| || ||||||||| | || || || |||
ctgaactattttttgtttcaaaactattgtaattctttgttgttttactatt-atttactccctgatatatatattctttcatatttgaaaaactat-tcagTTATGTGGCTCCGGAGTATGCAATGACGGGACATCTTCTTGTGAAGAGTGATGTTTACAGCTATGGTGTTGTCCTCCTTGAGCTTTTGACCGGAAGAAAA

upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G20590.1 (Glycine max), 3'ss of exon 9
------------gtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
|| | | | || | ||| || | |||| | |||| |||| | | |||| | | | ||| | | | | || || | |||||||||||||||||||||||||||||||| || |||||||||||||| || || || ||||| || |||||||| || || || || ||
ttaagttgttaggtgatgtcatttaaaaggttttat-ttcatctcttaacagttc-ctcaagatgaa-aactaaattcatctcattgacat-gttgttttgcagCTACTTAGCTCCTGAATATGCAATGACTGGCCATCTTCTGGTCAAGAGTGATGTTTATAGTTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG

upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G18470.1 (Glycine max), 3'ss of exon 8
gtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactca-tattacaaaattctggtca-attt-------ctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
| |||| | | | | | || | ||| | |||| || | || || ||| | || | | || ||| |||| | || ||| | || || || |||||||||||||| |||||||| || ||||| ||||||||||| || |||||||| || ||||||||| | || || || |||
ctgaactaattattgtttcaaaactattg-taattctttgttgttttactattatgccctccctgatatatattttctttcatatttgaaaaactattcagTTATGTGGCCCCAGAGTATGCAATGACTGGACATCTTCTTGTGAAGAGCGATGTTTACAGTTATGGTGTTGTCCTCCTTGAGCTTTTGACTGGAAGAAAA

upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G42600.1 (Glycine max), 3'ss of exon 4
--------gtatgctaaatctgaaattactat-ctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
|| || | | | | ||| | |||| ||| | | | || |||| || || ||| || | | | || ||| | ||||||||||||||||||||||| ||||| || || || ||||||||||||||||| || ||||| || |||||||| || | || || ||
agatcccggtgaacttttttttacacagatatacattaccatttctgtgcatttcctctagatgaaactgattttttgccattaaaatct-tgttttgcagCTATGTAGCTCCTGAATATGCAATGACTGGTCATCTCCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAAGTGGAAGAAAG

upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G01210.1 (Glycine max), 3'ss of exon 10
----------gtatgctaa-atctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
|| | || | ||| | || | |||| | | || | || | | | ||| | | ||| | | | | || || | |||||||||||||||||||||||||||||||| || |||||||| ||||| || || || ||||| || |||||||| || || || || ||
ttaagtggttaggtgatggcatgtaaaaggtttcatttcagctcttaacaattc-cttaaaatgaaaactgcat-tcatctcattgacat-gttgttttgcagCTACTTAGCTCCTGAATATGCAATGACTGGCCATCTTCTGGTCAAGAGTGACGTTTATAGTTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG

upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT5G56890.1 (Arabidopsis thaliana), 3'ss of exon 13
---gtatgctaaat-ctgaaattactatct-ttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
|| |||| | ||| || | |||| | || || | | | | ||| | || | || ||||| ||||||| | || || ||||| |||||||| || |||||| | || ||||||||||| || || ||||| ||||| ||||| ||||| ||||||||| |||||
gtaagataataaaaaccagaatcggtacaaactgcttcagactgttttttttcctgttccgattttaacttatataaat---gttgctttctaatagGTATGTGGCACCGGAATACGCAATGACAGGGCATCTTTTGGTGAAGAGTGATGTGTATAGTTACGGAGTTGTGCTTCTCGAGCTACTTACAGGGCGGAAA

upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0016g02150.t01 (Vitis vinifera), 3'ss of exon 11
-----------gtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
| | | || | || | | | ||| |||| | || || ||| || ||| | | |||| | | || | | |||||| | ||||| || ||||||||||||||||||||||| || |||||||||||||| ||||| || || || ||||||||||| || ||||| || |||
atattcctgctttctttaatatttttaagtcccctgtttgtgtcttttttttt--tttaattttat-gtctctgttctcctaattattattttttcccatcagGTATGTGGCTCCAGAGTATGCAATGACTGGCCATCTTCTTGTGAAGAGTGATGTTTATAGCTATGGAGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAA

upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv09s0002g02220.t01 (Vitis vinifera), 3'ss of exon 9
gtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactc--atattacaaaattctggtc-----aatttctctt-----agGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
||| | ||| || || || || |||| || | | | | || | || ||| ||| || || |||| | || || | ||||| |||||||||||||||||||||||||| || || |||||||||||||| || ||||| || ||||||||||| || ||||| || ||
-tatattttgcctgtggacggtagtttctttttctc---gttgttttattgctttgtgcttcaaaatctcaagtctcttatccaataaacttcttgttttccagCTACTTAGCTCCAGAATATGCAATGACTGGCCATCTTCTCGTGAAAAGTGATGTTTACAGTTATGGTGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAG

upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S343_14V6.1 (Physcomitrella patens), 3'ss of exon 7
--gtatgctaaatctgaaattactatcttt-acttcttcatagttgattcaataccatcaactcat-attacaaaatt--ctggtcaatttctctt--agGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
| | || | | |||| ||| | | | | | || | || | | | | ||| | | | ||| | |||||| | |||||| | || |||||||| |||||||| || ||||| || || ||||||||||||||||| ||||| || || ||||| ||||| || | || |||||
ttctcttgtattctcgtttcttctattttttagatatctttggctggaccgctagcgttgttacttgattcctgcacttactgattgatttctactgcagGTATGTGGCCCCTGAATACGCAATGACAGGGCATCTACTTGTGAAGAGTGATGTTTACAGTTACGGAGTAGTGCTTCTAGAGCTCCTCTCTGGACGGAAA

upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S79_45V6.1 (Physcomitrella patens), 3'ss of exon 7
----gtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaatt--ctggtcaatt---tctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
||| | || | | || || |||||| | | | | ||| | || | || ||| | | | | | | |||||| | || ||||||||||| ||||| ||||| ||||| |||||||| || || |||||||| || || || || ||||| |||||| | |||||||
accagta-gttatgagtccactttgtagctttacatagtaaaacggaccaagatattttttgcttgtcggaccaaagtgacaaattgaatcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG

upper sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S293_24V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------gtatgctaaatctgaaattactatctt-tacttct-----tcatagttgattcaatacc-atcaactcata-ttacaaaattctg-gtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
| | ||| || | | | | |||| || |||| | | || | | | | || || || || || ||| | || | || ||| | || ||| | || |||||||| || ||||| ||||| || ||||| ||||| || || |||||||| || || ||||||||||||||||| |||||||||
gtaggaactgcttttgtcatggtttttcagcacggagattaactc-gtgagtgcaatctaataattctggacgtttttgtgtacttattgcctattaaatcgtacttattagataatatgttaata---cgcagATATGTGGCGCCTGAATACGCGATGACAGGCCACCTCCTAGTGAAGAGCGACGTGTACAGCTATGGGGTGGTTCTTCTTGAGCTTCTCTCAGGGAGGATG

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|211520168|gb|FL238542.1|FL238542
EST:     TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGG                         GTATTTTGCTCCTGAATATGCAATGACTGGCCATC
genomic: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATC
EST: gi|101397928|gb|EB820841.1|EB820841
EST:     TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGG                         GTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
genomic: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
EST: gi|211132438|gb|FL443442.1|FL443442
EST:     TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGG                         GTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
genomic: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
EST: gi|211541315|gb|FL466512.1|FL466512
EST:     TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGG                         GTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
genomic: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
EST: gi|5268951|gb|AI770915.1|AI770915
EST:     TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGG                         GTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
genomic: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
EST: gi|211541314|gb|FL466511.1|FL466511
EST:     TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGG                         GTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA
genomic: TTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGA

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: 40 (upstream exon), 47 (downstream exon)
Score: 81

AACATGACTTCACCCCAAAGGTGTCAGACTTTGGCTTAGCAAGGACAGCTTTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 59

AACATGACTTCACCCCAAAGGTGTCAGACTTTGGCTTAGCAAGGACAGCTTTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 110

AACATGACTTCACCCCAAAGGTGTCAGACTTTGGCTTAGCAAGGACAGCTTTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 44

AACATGACTTCACCCCAAAGGTGTCAGACTTTGGCTTAGCAAGGACAGCTTTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTCATGGGAACTTTTGGgtatgctaaa ... tttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
 agttgat  putative branch site (score: 44)
 tttctctt  putative PPT
 tcatattacaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA