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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttttgaactaaaatgcagtatcaccaaaatatgcacattctgatttgtgaacacaactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG

Basic information

species Zea mays
transcript GRMZM2G137528_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 3
gtttgttttgaactaaaatgcagtatcaccaaa----atat-gcacattctgatttgtgaacacaactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG
|||||| |  || |  |||| | |||      |    |||| ||||||||||| |  ||||| ||||||| |||||||||| ||||| ||||||||||| || ||||||||||| |||||||||||||||||||||
gtttgtatataatttcaatgtactattgatgcatcgcatatagcacattctgactcatgaactcaacttttagGTCATTGAACTTCCTATCAAACATCCAGAGCTATTTGAGAGTCTTGGAATTGCCCAACCAAAG

upper sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------------------------------------------------------------------------gtttgttttgaactaaaatgcagtatcaccaaaatatgcacatt--------ctgatttgtg-aacacaactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG
                                                                                                                        || | ||||    ||  ||   | || || |||||  |   | |        || || | ||  |   ||  | |||||||||||| | |||||||||||||| || || ||||| || ||||||||||| |||||||||
gtatgttgcttgacattctttcggttttggcatttaaaattcgttctgtcaggagttagatattcttacctatccatgcatcactcgtgtgttaccttcctgtatgcatgtatctatcatgtatattttagtgtagcatcatgcattacaaaaatccgtttagtttttgggcctaatgtatgtgattaaatgtacagGTCATTGAGTTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG

upper sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------------------------------------------gtttgttttgaactaaaatgcagtatcaccaaaatatgcacatt--------ctgatttgtg-aacacaactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG
                                                                                                    | | ||||    ||  ||   | || |  |||||  |   | |        || || | ||  |   ||  | |||||||||||||| |||||||||||||| || || ||||| || ||||||||||| |||||||||
gtactttgcttgacattctttcaatgtcaggagttagatgcttttatctatccatgcatcactcgtgtgttacctttccgtgtgcatgtatctatctatttatattttagtgtagcatcatgcattagaaaaattagtttagtttttgaacctaatgtatgtgattaaatgtacagGTCATTGAGCTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG

upper sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------gtttgttttgaactaaaatgcagtatcaccaaaatatgcacattctg---atttgtgaacacaactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG
                                             || | | |   ||    ||    |||     ||| |  | ||  |    || | |   |     | ||||||||||||||| |||||||| ||||| ||| | ||||||   ||||||||||| || ||||||
gtatgcttagtgaatgagaaaccgaaactaaaagtcactacagtattggctatctcctctgttgtttcatccttttaatgtttatataatatctatatcttttctggtttatcagGTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAG

upper sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------------------------------------------------------gtttgttttgaactaaaatgcagtatcaccaaa----atatgcacattctgatttg------------tgaacacaactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG
                                                                                            ||  | |  |   ||     ||||| |  |     || | | |||| || |||             ||     | |||||||||||||||||||||||| ||||| || ||||| |||||||| |||||||| || |||||||||
gtttgtcctttgaccaattcttacatgttatttcattattattattaccattagcagcacttttaccttgatttaagttaggatttaaattcttaatctatagataagaaaggtatctcagatttttattttctcattttggtttaccttgtttttgttgtcttgatctttcagGTCATTGAGCTTCCAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAG

upper sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 3
---------------gtttgttttgaactaaaatgcagtatcaccaaaatatgcacattctgatttgtgaacacaactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG
               | || || |||  ||   |    | |     ||||       |  |    |||    | | | ||||||| ||||||||||||||||| ||||| ||| ||||||| || ||||| || || |||||||||
gttagctatatgagagcttcttctgattta---tttgttttggttgaaatccttctgtcttatgctgtct-taaacccttcagGTTATTGAGCTTCCAATCAAGCATCCTGAATTATTTGAAAGTCTTGGTATAGCTCAACCAAAG

upper sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ20576 (Selaginella moellendorffii), 3'ss of exon 3
gtttgttttgaactaaaatgcagtatcaccaaaatatgcacattctgatttgtgaacacaactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG
||  ||||||  |||   |    | || |    |  |  |  |||| ||||    |      | |||||| ||||||||||| ||||| ||||| || || ||||||||||| || ||||| || || |||
gtcagttttgg-ctatgct----tttcccttcgaggttaagtttcttatttc---atttctttctcagGTTATTGAGCTTCCGATCAAGCATCCTGAGCTTTTTGAGAGCCTGGGTATTGCACAGCCGAAG

upper sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 2
gtttgttttgaactaaaatgcagtatcaccaaaatatgcacattctgatttgtgaacacaactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG
||  ||||||  |||   |    | || |    |  |  |  |||| ||||    |      | |||||| ||||||||||| ||||| ||||| || || ||||||||||| || ||||| || || |||
gtcagttttgg-ctatgct----tttcccttcgaggttgagtttcttatttc---atttctttctcagGTTATTGAGCTTCCGATCAAGCATCCTGAGCTTTTTGAGAGCCTGGGTATTGCACAGCCGAAG

upper sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ28638 (Selaginella moellendorffii), 3'ss of exon 3
gtttgttttgaactaaaatgcagtatcaccaaaatatgcacattctgatttgtgaacacaactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG
||  ||||||       ||||  |  |     ||  || |  |||| ||||    |      | |||||| ||||||||||| ||||| ||||| || || ||||||||||| || ||||| || || |||
gtcagttttggct----atgcttttcccttcgaagttg-agtttcttatttc---atttctttctcagGTTATTGAGCTTCCGATCAAGCATCCTGAGCTTTTTGAGAGCCTGGGTATTGCACAGCCGAAG

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|32941875|gb|CF046694.1|CF046694
EST:     CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAG                         GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
genomic: CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
EST: gi|37393602|gb|CF634067.1|CF634067
EST:     AATTTAAGAGATCAAAGAG                         GTCA-TGAGCTTCCAATCAAACATCCGGAAATATTTGAGAGCC-TGGAATT
genomic: AATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
EST: gi|6989624|gb|AW447837.1|AW447837
EST:     TGGAGGTCTTGACCAGCAAATTAAAGAGATCAAAGAG                         GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
genomic: TGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
EST: gi|19350715|gb|BM895247.1|BM895247
EST:     CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAG                         GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
genomic: CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
EST: gi|211070411|gb|FL012986.1|FL012986
EST:     CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAG                         GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
genomic: CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
EST: gi|67024358|gb|CO453107.1|CO453107
EST:     CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAG                         GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
genomic: CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
EST: gi|19350732|gb|BM895264.1|BM895264
EST:     CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAG                         GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
genomic: CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
EST: gi|60395128|gb|DN227997.1|DN227997
EST:     CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAG                         GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
genomic: CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
EST: gi|32866277|gb|CF005959.1|CF005959
EST:     CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAG                         GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
genomic: CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
EST: gi|32933070|gb|CF037882.1|CF037882
EST:     CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAG                         GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT
genomic: CATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATT

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: 509

AGTTGATCCATTGGTCAATCTCATGAAAGTTGAGAAGGTTCCTGATTCTACATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 402

AGTTGATCCATTGGTCAATCTCATGAAAGTTGAGAAGGTTCCTGATTCTACATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 377

AGTTGATCCATTGGTCAATCTCATGAAAGTTGAGAAGGTTCCTGATTCTACATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 537

AGTTGATCCATTGGTCAATCTCATGAAAGTTGAGAAGGTTCCTGATTCTACATATGATATGATTGGAGGCCTTGACCAGCAAATTAAAGAGATCAAAGAGgtttgttttg ... caactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaatgcagtatcaccaaaatatgcacattctgatttgtgaacacaactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG
                                                ctttc  CT-rich tract
                 aaaatat  TA-rich tract