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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggttctctcgaagttccatgaggtggcacgggagacgtttgaatgcttgggcgtgtgtgtgttgtgaagctgggaaaggtttttaggcattatttggtataatgccagggttttaaagtaagagggagtcatggtgtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAGACAAGCCGTGGATATTTCCCCTCTGAGGAGGGTAAACCAAGCTATCTAC

Basic information

species Physcomitrella patens
transcript PP1S101_208V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S101_208V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G156673_T02 (Zea mays), 3'ss of exon 1
gtgggttctctcgaagttccatgaggtggcacgggagacgtttgaatgcttgggcgtgtgtgtgttgtgaagctgggaaaggtttttaggcattatttggtataatgccagggttttaaagtaagagggagtcatggtgtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAGACAAGCCGTGGATATTTCCCCTCTGAGGAGGGTAAACCAAGCTATCTAC
                                         |    |||||  |  | || |     |  ||||    |      |||    ||   | ||   |||  |   | ||   || |   |  |  || || |   ||||||||||| ||||||||||| || ||||| || |||||||| ||| | ||||| || ||||||||||| || || ||||||||||| ||||| || ||||||
----------------------------------------gtcatgtgcttttg-atatgggaaac-tatagctcaatatatagcttacatgttgggtcgtgagatgtgaaactgtt---gtgatgtgctgctattgtct---tgcagTGGACCCCGTGAGGATGCCACCCGTATTGGTTCCGCTGGTGTTGTGAGGAGGCAGGCCGTGGATATCTCACCCCTGAGGAGGGTGAACCAGGCCATCTAC

upper sequence: PP1S101_208V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G078985_T01 (Zea mays), 3'ss of exon 2
gtgggttctctcgaagttccatgaggtggcacgggagacgtttgaatgcttgggcgtgtgtgtgttgtgaagctgggaaaggtttttaggcattatttggtataatgccagggttttaaagtaagagggagtcatggtgtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAGACAAGCCGTGGATATTTCCCCTCTGAGGAGGGTAAACCAAGCTATCTAC
                                         ||   ||||  |   |||      | | |  |     |  | ||  |    ||   |  |   ||| ||   |      ||     |   | ||  |||   ||||||||||| ||||||||||| || ||||| || || ||||| ||| | || || || || |||||||| || || ||||| ||||| ||||| || ||||||
-----------------------------------------ttatgtgctatgagatgtcaac--tataactcaaactattgattacacatgttggctcttgagatgtcaaact-----ggtgttctgtgctgatattgtctttgcagTGGACCACGTGAGGATGCCACCCGTATTGGTTCAGCTGGTGTTGTGAGAAGGCAGGCTGTGGATATCTCACCCCTGAGAAGGGTGAACCAGGCCATCTAC

upper sequence: PP1S101_208V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ17708 (Selaginella moellendorffii), 3'ss of exon 3
gtgggttctctcgaagttccatgaggtggcacgggagacgtttgaatgcttgggcgtgtgtgtgttgtgaagctgggaaaggtttttaggcattatttggtataatgccagggttttaaagtaagagggagtcatggtgtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAGACAAGCCGTGGATATTTCCCCTCTGAGGAGGGTAAACCAAGCTATCTAC
                                                                               ||   | |||    | |||| || ||   ||  | |||   ||         || || |     |||||||| |||||||| ||||||||||| ||||| |||||||| ||  | ||| | || || || ||||| || |||||| |  | || || ||||| || |||
-----------------------------------------------------------------------------gtagagctatagat-ctctttgttacaacttcattgatttttcgtcct------tcctgct-----tgcagTGGTCCTCGTGAAGATGCTACACGAATCGGTTCCGCTGGTGTGGTGAGGCGTCAGGCTGTTGATATCTCGCCTCTGCGTCGCGTGAATCAAGCCATTTAC

upper sequence: PP1S101_208V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ16239 (Selaginella moellendorffii), 3'ss of exon 3
gtgggttctctcgaagttccatgaggtggcacgggagacgtttgaatgcttgggcgtgtgtgtgttgtgaagctgggaaaggtttttaggcattatttggtataatgccagggttttaaagtaagagggagtcatggtgtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAGACAAGCCGTGGATATTTCCCCTCTGAGGAGGGTAAACCAAGCTATCTAC
                                                                               ||   | |||    | |||| || ||   ||  | |||   ||         || || |     |||||||| |||||||| ||||||||||| ||||| |||||||| ||  | ||| | || || || ||||| || |||||| || | || || ||||| || |||
-----------------------------------------------------------------------------gtagagctatagat-ctctttgttacaacttcattgatttttcgtcct------tcctgct-----tgcagTGGTCCTCGTGAAGATGCTACACGAATCGGTTCCGCTGGTGTGGTGAGGCGTCAGGCTGTTGATATCTCGCCTCTGCGGCGCGTGAATCAAGCCATTTAC

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|37850596|gb|BJ608604.1|BJ608604
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|37839850|gb|BJ597858.1|BJ597858
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|162237504|gb|FC413613.1|FC413613
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|67720078|gb|BJ970337.1|BJ970337
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCACCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|18362582|gb|BJ194653.1|BJ194653
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|18338455|gb|BJ170479.1|BJ170479
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|162236998|gb|FC412949.1|FC412949
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|37839339|gb|BJ597347.1|BJ597347
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|67696498|gb|BJ956731.1|BJ956731
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|67725656|gb|BJ975915.1|BJ975915
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|162243879|gb|FC423196.1|FC423196
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|67696110|gb|BJ956343.1|BJ956343
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|162243102|gb|FC416702.1|FC416702
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|67697648|gb|BJ957881.1|BJ957881
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|162241814|gb|FC418069.1|FC418069
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|18361640|gb|BJ193706.1|BJ193706
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|67572736|gb|BJ945560.1|BJ945560
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|67726461|gb|BJ976720.1|BJ976720
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|67717134|gb|BJ967393.1|BJ967393
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|67574244|gb|BJ947068.1|BJ947068
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|18369285|gb|BJ201370.1|BJ201370
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCANGAN
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|162243878|gb|FC423195.1|FC423195
EST:     CTGACCGACCAGAACCCTATCCAGGTCATGGTGGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|67573113|gb|BJ945937.1|BJ945937
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|18368029|gb|BJ200113.1|BJ200113
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|162243101|gb|FC416701.1|FC416701
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|67717958|gb|BJ968217.1|BJ968217
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
EST: gi|162266196|gb|FC441725.1|FC441725
EST:     CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAG                         TGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG
genomic: CTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAG

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: 34 (upstream exon), 35 (downstream exon)
Score: 22

AGTTGATGGCTGTACGCATCGTGAAGCACGCGATGGAGATTATTCACCTACTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctc ... gtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAGACAAGCCGTGGATATTTCCCCTCTGAGGAGGGTAAACCAAGCTATCTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttggtataatgccagggttttaaagtaagagggagtcatggtgtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAGACAAGCCGTGGATATTTCCCCTCTGAGGAGGGTAAACCAAGCTATCTAC
                    ttttaaagtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggttctctcgaagttccatgaggtggcacgggagacgtttgaatgcttgggcgtgtgtgtgttgtgaagctgggaaaggtttttaggcattatttggtataatgccagggttttaaagtaagagggagtcatggtgtgagtgcagTGGACCTCGTGAGGATGCTACACGTATCGGATCCGCTGGAGTTATCAGGAGACAAGCCGTGGATATTTCCCCTCTGAGGAGGGTAAACCAAGCTATCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT