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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcattttgtagacgttatagtttcacttgttcagtatggccatctacttttctccatatgccatctgtagcaccttacttttggttcatatttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTTAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCTC

Basic information

species Zea mays
transcript GRMZM2G128121_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128121_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 3'ss of exon 11
gtaattcattttgtagacgttatagtttcacttgttcagt--atggc-catctacttttct--ccatatgccatctgtagcaccttacttttggttcatatttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTTAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCTC
|| || || ||  || ||  | ||  |||| |     | |  ||    |||| |  |||    ||| || |           ||||| ||||   |  ||||||   | ||||||| |||||||| || || |||||||||||||||||| |||| |||||||||||||| ||||| ||  ||||||||||  |||| ||| | ||||| |
gtgat-cacttgttaaacaatttatgttcagtataataatctataatgcatcaatcttttcaaccacatactgcaaaagtttccttattttttactgctatttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCATCTGTTAGAAAAACAAATAGATTGGTGACCATTGAGGAAAGCTTCCCAC

upper sequence: GRMZM2G128121_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 11
gtaattcattttgtagacgttatagtttcacttgttcagtatggccatctacttttctccatatgccatctgtagcaccttacttttggttcatatttgttg----acagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTTAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCTC
                  || | | |||   || |   | |    |  |  |||||    | |   ||| ||    | | || |  ||  | || ||  |      | |||| || ||  | || || ||| | || |||||| || |  | || ||||| ||||| |||||||||||| |  ||||||| |||||||||||||| ||||
------------------gtaaaactttagtttataatgaactttccccctcttttgcaaaaacttcatttgggttatcataatggtgagtgatgttcttatccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTC

upper sequence: GRMZM2G128121_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G46380.2 (Glycine max), 3'ss of exon 11
gtaattcattttgtagacgttatagtttcacttgttcagtatggccatctacttttctccatatgccatctgtagcaccttacttttggttcatatt--tgttgaca--gGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTTAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCTC
                  || | |  ||   || |   | |   ||  |   ||||    | |   ||| ||    |   || |  ||  | || ||  |||  |||  ||| || ||  | || || ||| | ||||||||| || |  | || ||| | ||||| |||||||||||| |  ||||||| |||||||||||||| ||||
------------------gtaaaacattagtttataatgaacttccccccttttttgcagaaacttcatttgggttatgatagtggtgagtgatgttcttgtccacacagGTCATTAATTTGCGTTCAATCCGGCCACTTGATCGATCCACAATCAATACTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTC

upper sequence: GRMZM2G128121_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA14G02380.1 (Glycine max), 3'ss of exon 11
gtaattcattttgtagacgttatagtttcacttgttcagtatggccatctacttttctccatatgccatctgtagcaccttacttttggttcatatt--tgttgaca--gGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTTAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCTC
                  || | | |||   ||||   | |   ||      ||||    |     ||| ||    |   || |  ||  | ||  |  | |  |||  ||| || ||  | || || ||| |||| |||||| |  |  | || ||| | ||||| |||||||||||| |  ||||||| |||||||||||||| ||||
------------------gtaaaactttagtttgtaatgaacttcccctcttttttgcaaaagcatcatttgggttatgataatggtgagtgatgctcttatccacatagGTCATTAATTTGCGTTCAATCCGACCGCTTGATCGGTCCACAATCAATACTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTC

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|78115877|gb|DV534265.1|DV534265
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|148971222|gb|EE022081.2|EE022081
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|110220018|gb|EC901916.1|EC901916
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|78104220|gb|DV522638.1|DV522638
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|24769217|gb|CA404346.1|CA404346
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         ATGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|71325375|gb|DR799361.1|DR799361
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|93013442|gb|EB638962.1|EB638962
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|71331066|gb|DR802363.1|DR802363
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|32856323|gb|CD996004.1|CD996004
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|33942400|gb|CF349000.1|CF349000
EST:     ACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: ACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|211386006|gb|FL329690.1|FL329690
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAAAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|211417439|gb|FL345693.1|FL345693
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|71429465|gb|DR810515.1|DR810515
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|149109553|gb|EE293365.2|EE293365
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|60341592|gb|DN208565.1|DN208565
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|4730273|gb|AI649439.1|AI649439
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|78081841|gb|DV510253.1|DV510253
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|18661120|gb|BM501222.1|BM501222
EST:     CAGGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: CAGGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|78180140|gb|DV550513.1|DV550513
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|12045820|gb|BF727959.1|BF727959
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|31348876|gb|CD433233.1|CD433233
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|76290822|gb|DV030390.1|DV030390
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|211179193|gb|FL462626.1|FL462626
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAAAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|76021492|gb|DT948662.1|DT948662
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|6859967|gb|AW355961.1|AW355961
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|71762956|gb|DR960893.1|DR960893
EST:     GAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCA

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: 45 (upstream exon), 49 (downstream exon)
Score: 197

GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTTAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 205

GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTTAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCTC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 157

GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTTAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 488

GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcatt ... ttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTTAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttctccatatgccatctgtagcaccttacttttggttcatatttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTTAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCTC
                         accttac  putative branch site (score: 488)
                                      ttcatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattcattttgtagacgttatagtttcacttgttcagtatggccatctacttttctccatatgccatctgtagcaccttacttttggttcatatttgttgacagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTTAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG