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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_16V6.2
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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaatggctctggttgctggatcgatcgctaagccgtggtaaccgaaattggcagGATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTTGGCGTTACATGCCGAACCACGCCATGACCCCCCATATCTCCGGCACGAC
                                    tggtaac  putative branch site (score: 2)
                                             aaatt  TA-rich tract