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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatttccccttctgtttgtctaactatatattgttttttcttaacatttgtatgcttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT

Basic information

species Zea mays
transcript GRMZM2G028089_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028089_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g39070.1 (Oryza sativa), 3'ss of exon 4
gtaagtatttcccct---tctgtttgtctaactatatattgtttttt------cttaacatttgtatgcttgata-aaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT
|| ||| |||  | |   | ||||  | |  | ||| ||  |||||       |||||| || ||| | |||||  ||||||||||||||| |||||||||||||| || |||||||||||||||||||||||||||||||| || || || ||||| |
gttagtttttttcttgtgtgtgttgctttttccataaataatttttgttaagacttaacgttagtacgtttgatttaaagACTGTAGAGGCAGAGAGGATATCTGTTGATCATGTTGCCCATCTCAAACCATCTGATGGTGGCTCTGCGGCGACTCAAT

upper sequence: GRMZM2G028089_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 4
-----------------------------------------gtaagtatttccccttctgtttgtctaactatatattgttttttcttaacatttgtatgcttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT
                                          | | | ||||    | |  |||  | ||| |  |||   || | |   | |     |||||     |||||||| || || ||  ||||||| || || |||||||| ||||| || |||||||||||||||||||| || || || |
gttggattttatgacttcttctatcccttttcacattttaaatcactgtttctaaat-taattgattgact-tggattcccttctatcctcctcctcttgctttgctgaagACTGTTGAAGCAGAACGGATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT

upper sequence: GRMZM2G028089_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 4
-----------------------------------------gtaagtatttccccttctgtttgtctaactatatattgttttttcttaacatttgtatgcttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT
                                          | | | |||| |  |   ||  |  |  |  ||    || | |||   | |    ||||||     |||||||| || || ||  | ||||| || || |||||||| ||||| || |||||||||||||||||||| || || || |
gttgggttttatgacttctgctatcccttttcacattttaaatcactgtttctcaattaattgattcacttggattcccttctctctc--cctcctcatgctttgctgaagACTGTTGAAGCAGAACGAATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT

upper sequence: GRMZM2G028089_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtatttc--cccttctgtttgt---ctaactatatattgt---------tttttcttaacatttgtatgcttgataaa------agACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT
||| || |||   ||  |   | |||   ||| |||| |  | |          |||   |||||||   ||| |||  ||       |||| || || ||||| || |||||||| || |||||||| ||||| || ||||||||||| || ||||| || |||||||
gtatgtgtttaggccacttgatctgtaatctatctatgtgatatgagagtggactttcaataacattgcaatgattgtaaacgcgtgcagACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT

upper sequence: GRMZM2G028089_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------gtaagtatttccccttctgtttgtctaactatatattgttttttct-----------------------taacatttgtatgcttgataaaa----gACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT
                      | || || ||    || | |||||| |||  | |    |||  |||                       ||| ||||  | |  | ||| ||    ||| || || |||||  ||||||| || || |||||||| ||||| ||||||||||| || || ||||||||||| ||||
gtctgtgcttaagtttgattctgcaaataattttttttttttttgtcaaacattctgcaatttaatctatgttatgaaagtgtacattgactaagattttgaggtgttatacaatgtagACAGTTGAAGCTGAACGGATATCAGTTGATCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGT

upper sequence: GRMZM2G028089_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtatttccccttctgtttgtctaactatatattgttttttcttaac------------att-tgtatgcttgata-aaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT
||  |  || | | |  | ||| | |||  |||| |    | |    |||            ||| | | | |||| |  |||||| ||||| || || ||||| || || || |||||||| ||||| |||||||||||||| ||||| || |||||||| |
gttcgacttgctcttcttttttttttaatcatatttcacctatcaccaactggggtaactgaattattttttcttgtttcaaagACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAAT

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|5343228|gb|AI795413.1|AI795413
EST:     TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
genomic: TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAGgtaagtattt ... ttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
EST: gi|74245516|gb|DT653430.1|DT653430
EST:     TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
genomic: TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAGgtaagtattt ... ttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
EST: gi|148964739|gb|EC906002.2|EC906002
EST:     TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
genomic: TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAGgtaagtattt ... ttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
EST: gi|71427075|gb|DR808125.1|DR808125
EST:     TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
genomic: TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAGgtaagtattt ... ttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
EST: gi|78079914|gb|DV508326.1|DV508326
EST:     TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
genomic: TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAGgtaagtattt ... ttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
EST: gi|71428766|gb|DR809816.1|DR809816
EST:     TCGATGGGTGTCCTCAGCTTATTTTTGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
genomic: TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAGgtaagtattt ... ttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
EST: gi|71428767|gb|DR809817.1|DR809817
EST:     TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
genomic: TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAGgtaagtattt ... ttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
EST: gi|78079913|gb|DV508325.1|DV508325
EST:     TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
genomic: TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAGgtaagtattt ... ttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
EST: gi|78104235|gb|DV522653.1|DV522653
EST:     TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
genomic: TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAGgtaagtattt ... ttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
EST: gi|5650012|gb|AI920372.1|AI920372
EST:     TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
genomic: TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAGgtaagtattt ... ttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
EST: gi|76925807|gb|DV170603.1|DV170603
EST:     TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
genomic: TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAGgtaagtattt ... ttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
EST: gi|74245515|gb|DT653429.1|DT653429
EST:     TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAG                         ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA
genomic: TCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAGgtaagtattt ... ttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCA

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: 65

AGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAGgtaagtattt ... ttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT


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

AGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAGgtaagtattt ... ttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT


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

AGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAGgtaagtattt ... ttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 54

AGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAGgtaagtattt ... ttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtttgtctaactatatattgttttttcttaacatttgtatgcttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT
          taactatatattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatttccccttctgtttgtctaactatatattgttttttcttaacatttgtatgcttgataaaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG