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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactcgacaacttccgaaaacttccgctcatcccctgcatgtcgctaacctagaatcctaggcttgcttaccaggaacatgaacaccaatcacgaatggctctggttgctggatcgatcgctaagccgtggtaaccgaaattggcagGATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTTGGCGTTACATGCCGAACCACGCCATGACCCCCCATATCTCCGGCACGAC

Basic information

species Physcomitrella patens
transcript PP1S106_16V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S106_16V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G170602_T01 (Zea mays), 3'ss of exon 4
-------------------gtaac-tcgacaacttccgaaaacttccgctcatcccctgcatgtcgctaacctagaatcct----aggcttgcttaccaggaacatgaacaccaa----tcacgaatggctctggttgctggatcgat---cgctaagccgtggtaaccgaaattggcagGATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTTGGCGTTACATGCCGAACCACGCCATGACCCCCCATATCTCCGGCACGAC
                   ||  | ||  ||  ||| |     |  |     |   |  |||| ||| ||   |||| | |    ||||  |     |||    |  |    | |    |    ||  ||  || | ||  ||   ||       || | || |||  ||  ||   ||||||| || || ||||| ||| || ||||||| ||    |||||||| || ||||| |||||||| ||| ||||||||||||| || ||||||||||| ||
gtatgtactggctgctgctgtgtcctcctcattttcagcgggttagcatctgttagcaccatggcgccaaaacagaagcttgaagaggcgggtcgtgcagaggaagaagtggcgagatatagaaaaacgccatgctcgccagactcatacgtctcaaactgttgtatgcgtgatgatcagGATACGGCGGCGATGTGTGGCACCCTCAGCCTGCGCCCAAGGACCACCCGTGGCGCTACATGCCCAACAACGCCATGACCCCTCACATCTCCGGCACCAC

upper sequence: PP1S106_16V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA19G01200.1 (Glycine max), 3'ss of exon 4
gtaactcgacaacttccgaaaacttccgctcatcccctgcatgtcgctaacctagaatcctaggcttgcttaccaggaacatgaacaccaatcacgaatggctctggttgctggatcgatcgctaagccgtggtaaccgaaattggcagGATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTTGGCGTTACATGCCGAACCACGCCATGACCCCCCATATCTCCGGCACGAC
                                             | |     | | ||| |     | |   |||       ||       ||  |      ||  ||| |   |    |  |    |    |  |  ||||    ||| ||||| || ||||| |||  |   || || ||   |||||||||||| ||||| |||||||| ||||| |||||||| || ||||| || ||||| ||
---------------------------------------------gtttgttcatattcccatctaagttgttcagaggtggcaaagttttacatcatcattgctaattgttttcttttccttt----ccaaatttcttaaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCATGGCGCTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC

upper sequence: PP1S106_16V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA13G23790.4 (Glycine max), 3'ss of exon 4
gtaactcgacaacttccgaaaacttccgctcatcccctgcatgtcgctaacctagaatcctaggcttgcttaccaggaacatgaacaccaatcacgaatggctctggttgctggatcgatcgctaagccgtggtaaccgaaattggcagGATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTTGGCGTTACATGCCGAACCACGCCATGACCCCCCATATCTCCGGCACGAC
                                           || ||||  |    |   |  |||  ||      |  ||      |  |    | | ||  |   |  |    | ||| ||    | |  |  |  |  |    ||| ||| | || ||||| |||  | | ||||| ||   |||||| ||||| |||||||||||||| ||||| |||||||| || ||||| || ||||| ||
-------------------------------------------tccctaagttctgttatgatcctttgttgttgttactat-----tcctttttaagttgcaattactaattttgccatc-ctctttcctaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC

upper sequence: PP1S106_16V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv14s0066g01320.t01 (Vitis vinifera), 3'ss of exon 4
gtaactcgacaacttccgaaaacttccgctcatcccctgcatgtcgctaacctagaatcctaggcttgcttaccaggaacatgaacaccaat--cacgaatggctctggttgctggatcgatcgctaagccgtggtaaccgaaattggcagGATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTTGGCGTTACATGCCGAACCACGCCATGACCCCCCATATCTCCGGCACGAC
                                          ||       |   | |  |  | ||  |      ||  |||     ||||    |   |    | | ||       | ||  ||      |  |   |  | ||  |||| ||  | || ||||| ||| |  | ||||| ||    ||||||||||| ||||| |||||||| ||||| || |||||||| ||||| || ||||| ||
------------------------------------------gtaatgtttcagcacttttgagtttcttggatttgagtatgttgttcaatgtttctttttatgcagttttgaaagccaatgacttcattttaattttctgatttt-cagGTTACAGTGGGGATGTTTGGTATCCACAGCCAGCCCCCAAGGACCATCCATGGCGGTACATGCCAAACCAAGCTATGACCCCTCATATTTCTGGCACCAC

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|208385885|gb|DC956723.1|DC956723
EST:     TGCAGATACGGAGGCAGTGAAAGAAGCATGCGAGTCAGGACACCTCGGAG                         GATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTT
genomic: TGCAGATACGGAGGCAGTGAAAGAAGCATGCGAGTCAGGACACCTCGGAGgtaactcgac ... aaattggcagGATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTT
EST: gi|162269932|gb|FC445423.1|FC445423
EST:     TGCAGATACGGAGGCAGTGAAAGAAGCATGCGAGTCAGGACACCTCGGAG                         GATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTT
genomic: TGCAGATACGGAGGCAGTGAAAGAAGCATGCGAGTCAGGACACCTCGGAGgtaactcgac ... aaattggcagGATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTT
EST: gi|18335876|gb|BJ167897.1|BJ167897
EST:     TGCAGATACGGAGGCAGTGAAAGAAGCATGCGAGTCAGGACACCTCGGAG                         GATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTT
genomic: TGCAGATACGGAGGCAGTGAAAGAAGCATGCGAGTCAGGACACCTCGGAGgtaactcgac ... aaattggcagGATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTT
EST: gi|18341708|gb|BJ173743.1|BJ173743
EST:     TGCAGATACGGAGGCAGTGAAAGAAGCATGCGAGTCAGGACACCTCGGAG                         GATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTT
genomic: TGCAGATACGGAGGCAGTGAAAGAAGCATGCGAGTCAGGACACCTCGGAGgtaactcgac ... aaattggcagGATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTT
EST: gi|208345467|gb|DC917350.1|DC917350
EST:     TGCAGATACGGAGGCAGTGAAAGAAGCATGCGAGTCAGGACACCTCGGAG                         GATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTT
genomic: TGCAGATACGGAGGCAGTGAAAGAAGCATGCGAGTCAGGACACCTCGGAGgtaactcgac ... aaattggcagGATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTT
EST: gi|208386186|gb|DC949097.1|DC949097
EST:     TGCAGATACGGAGGTAGTGAAAGAAGCATGCGAGTCAGGACACCTCGGAG                         GATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTT
genomic: TGCAGATACGGAGGCAGTGAAAGAAGCATGCGAGTCAGGACACCTCGGAGgtaactcgac ... aaattggcagGATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTT
EST: gi|67697753|gb|BJ957986.1|BJ957986
EST:     TGCAGATACGGAGGCAGTGAAAGAAGCATGCGAGTCAGGACACCTCGGAG                         GATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTT
genomic: TGCAGATACGGAGGCAGTGAAAGAAGCATGCGAGTCAGGACACCTCGGAGgtaactcgac ... aaattggcagGATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTT
EST: gi|162262253|gb|FC437164.1|FC437164
EST:     TGCAGATACGGAGGCAGTGAAAGAAGCATGCGAGTCAGGACACCTCGGAG                         GATATGGAGGAGATGTATGGAACGCTCAGCCGGCA
genomic: TGCAGATACGGAGGCAGTGAAAGAAGCATGCGAGTCAGGACACCTCGGAGgtaactcgac ... aaattggcagGATATGGAGGAGATGTATGGAACGCTCAGCCGGCA
EST: gi|162272578|gb|FC448542.1|FC448542
EST:     TGCAGATACGGAGGCAGTGAAAGAAGCATGCGAGTCAGGACACCTCGGAG                         GATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTT
genomic: TGCAGATACGGAGGCAGTGAAAGAAGCATGCGAGTCAGGACACCTCGGAGgtaactcgac ... aaattggcagGATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTT

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: 35 (upstream exon), 35 (downstream exon)
Score: 60

GCGAAGATGAAGAAGGGAGCTTATCTGGTGAACAACGCGCGAGGAGCCATTGCAGATACGGAGGCAGTGAAAGAAGCATGCGAGTCAGGACACCTCGGAGgtaactcgac ... aaattggcagGATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTTGGCGTTACATGCCGAACCACGCCATGACCCCCCATATCTCCGGCACGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaatggctctggttgctggatcgatcgctaagccgtggtaaccgaaattggcagGATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTTGGCGTTACATGCCGAACCACGCCATGACCCCCCATATCTCCGGCACGAC
                                    tggtaac  putative branch site (score: 60)
                                             aaatt  TA-rich tract