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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcatgaatcgtgtgccgtcatgtcattctgccgctaattaatgtgtccacaagtattctgagcttgacgccaaggcatgtggcgagcgtgatgctctgagcttagcagttctgaggaacggtgcctcatgcacgtggaatggtggaatgttgtgcgacagCTTGGTACATATGAAAAAGAGCTGGAGGAGATGAAGAACATGTCTCGGCAGGAGTATGTGGCCTCGTTGAGGAG

Basic information

species Physcomitrella patens
transcript PP1S131_139V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os07g03250.1 (Oryza sativa), 3'ss of exon 3
gtaagtcatgaatcgtgtgccgtcatgtcattctgccgctaattaatgtgtccacaagtattctgagcttgacgccaaggcatgtggcgagcgtgatgctctgagcttagcagttctgaggaacggtgcctcatgcacgtggaatggtggaatgttgtgcgacagCTTGGTACATATGAAAAAGAGCTGGAGGAGATGAAGAACATGTCTCGGCAGGAGTATGTGGCCTCGTTGAGGAG
                                                       || || ||  |  |  |    ||    | ||          | || | |  | |  ||||  |   ||  |       |||| |   |    || |    |||  | ||||| |     ||  |  | |||||||||||||||||||||||| |  ||||||||||||||||    || |||||
-----------------------------------------------------gtaattaatc--aattcaat--taaaatttttgattctgtaagtactgttaattaattagtt--ggttaattgaataatgtgcatgcatatgtatgta----tgtatg-cagCTGGAGGACTACCAGGAGGAGCTGGAGGAGATGAAGAACATGACAAGGCAGGAGTATGTGGCTCACTTAAGGAG

upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 4
----gtaagtcatgaatcgtgtgccgtcatgtcattctgccgctaattaatgtgtccacaagtattctgagcttgacgccaaggcatgtggcgagcgtgatgctctgagct-tagcagttctgaggaacggtgcctcatgcacgtggaatggtggaatgttgtgcgacagCTTGGTACATATGAAAAAGAGCTGGAGGAGATGAAGAACATGTCTCGGCAGGAGTATGTGGCCTCGTTGAGGAG
     ||| | |  ||   ||    ||    |  ||      ||    |      |   |   ||| |    | ||    |  |    | ||    | |   || |||      | |||| ||| |    |    ||||  ||||    |      || || || | ||| | |     ||  |  | ||||||||||||||||||||||||    ||||||||||||||||     | || ||
gtgattaaattaccaactctgattagttcatttgttgcttttcttgcaagcaaa-cagtacacattttagtttagattttagagtgc-tagctcaag-ggcactgtgaatgactgtagttatgatgttacggctatcattgacgtttgttttcaccattttctg-ggcagTTGGAGGACTACCAGGAGGAGCTGGAGGAGATGAAGAACATGAGCAGGCAGGAGTATGTGGCTCACCTCAGAAG

upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os01g67410.1 (Oryza sativa), 3'ss of exon 5
gtaagtcatgaatcgtgtgccgtcatgtcattctgccgctaattaatgtgtccacaagtattctgagcttgacgccaaggcatgtggcgagcgtgatgctctgagctta-gcagttctgaggaacggtgcctcatgcacgtggaatggtggaatgttgtgcgacagCTTGGTACATATGAAAAAGAGCTGGAGGAGATGAAGAACATGTCTCGGCAGGAGTATGTGGCCTCGTTGAGGAG
                               | ||    |||||||| |    |||  |  | | |  |||         ||       |   |||| ||  || ||   | | |  |||  |      |   |   |   | ||||||       | |    ||| |   ||  |||||||| |||||||||||||||||| ||||| |  |||||||||  || ||||| ||||| ||
------------------------------gtgtgtttataattaatat----acagattgtgtcacattgttattttctcactcttttatt-tgatact--gatctagtgtaatgatgattactaaaactgtacttaaaggcaatggttt--ctgtatttttcagGTAAATAACTATGAAAAGGAGCTGGAGGAGATGAAGCACATGACAAGGCAGGAGTTCGTAGCCTCTTTGAGAAG

upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G146688_T01 (Zea mays), 3'ss of exon 5
gtaagtcatgaatcgtgtgccgtcatgtcattctgccgctaattaatgtgtccacaagtattctgagcttgacgccaaggcatgtggcgagcgtgatgctctgagcttagcagttctgaggaacggtgcctcatgcacgtggaatggtggaatgttgtgcgacagCTTGGTACATATGAAAAAGAGCTGGAGGAGATGAAGAACATGTCTCGGCAGGAGTATGTGGCCTCGTTGAGGAG--------------------------
                                               ||    |    | || ||   |||       |   ||   |  | || |   ||  | | | || |  ||||   || ||||  | ||   |        || ||   ||   || |||| |     ||  |  | |||||||||||||||||||||||| | ||||||||||| |||||     | |||||                          
-----------------------------------------------gtaataattttttttttgcttttgttttaccgtggtgcatcatg-gtaaaaatcctaccattgctgcgctgat--actgtgctgcgtgtgtgcc------tgcaac-ctgaatga-agCTGGAGGACTACCAGGAGGAGCTGGAGGAGATGAAGAACATGACACGGCAGGAGTACGTGGCGCACCTCAGGAGGTACGTACGTACGTCGTTTCACTTCA

upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G008234_T01 (Zea mays), 3'ss of exon 2
gtaagtcatgaatcgtgtgccgtcatgtcattctgccgctaattaatgtgtccacaagtattctgagcttgacgccaaggcatgtggcgagcgtgatgctctgagcttagcagttctgaggaacggtgcctcatgcacgtggaatggtggaatgt---tgtgcg-acagCTTGGTACATATGAAAAAGAGCTGGAGGAGATGAAGAACATGTCTCGGCAGGAGTATGTGGCCTCGTTGAGGAG
                                                             |  | || |||  |    ||       ||| | | ||  |||||||||   || ||    ||   ||  | ||  |      |||   | ||||     ||||  ||||| |     ||  |  | |||||||||||||||||||||||| | ||||||||||| |||||     | |||||
-------------------------------------------------------------tgcgtgcctgatactgttgc------tgagggagctgagctgagcttatt-gtactatataataatggtt-ataaaaaaaacatgtctgcatgtgtgcctgcgtgcagCTGGAGGACTACCAGGATGAGCTGGAGGAGATGAAGAACATGACGCGGCAGGAGTACGTGGCGCACCTCAGGAG

upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G028151_T02 (Zea mays), 3'ss of exon 2
gtaagtcatgaatcgtgtgccgtcatgtcattctgccgctaattaat-gtgtccacaagtattctgagcttgacgccaaggcatgtggcgagcgtgatgctctgagcttagcagttctgaggaacggtgcctcatgcacgtggaatggtggaatgttgtgcgacagCTTGGTACATATGAAAAAGAGCTGGAGGAGATGAAGAACATGTCTCGGCAGGAGTATGTGGCCTCGTTGAGGAG
                                       |||| ||  |    ||    || ||||||  |||       |  |||   |  |   |||   || ||| |       ||| || |   |  |  | ||  |  |   |  |   |  ||    ||| | |     ||     |||||||||||||||||||||||||| |  | |||||||| || ||     |||| ||
--------------------------------------gtaatgaaccgaagacaacgatagtctgagtctgagaatggtgt-tgtcttgttcacaatg---tgtgctga------ttgatgatcttggtgttgtccattttaacgcgccgcgcggagt----cagGTGGAGGACTACAGGGAAGAGCTGGAGGAGATGAAGAACATGACCAGACAGGAGTACGTCGCTCACCTGAGAAG

upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G399072_T03 (Zea mays), 3'ss of exon 4
gtaagtcatgaatcgtgtgccgtcatgtcattctgccgctaattaatgtgtccacaagtattctgagcttgacgccaaggcatgtggcgagcgtgatgctctgagcttagcagtt-ctgaggaacggtgcctcatgcacgtggaatgg--tggaatgttgtgcgacagCTTGGTACATATGAAAAAGAGCTGGAGGAGATGAAGAACATGTCTCGGCAGGAGTATGTGGCCTCGTTGAGGAG
                                                            |||     |   || |    |||| |     | | || ||   |  | |  | |  |||    ||| | ||| || |||        |     |||  ||  ||  ||||  |    || || || |||||||||||||||||| |||||||  |||||||||   | ||     |||| ||
------------------------------------------------------------ttcactattcatcgtc----catgcgct---ctttattcttgcatttgatgaatggctggtacacgtttcctgatccactgacctccgatctaaataatgcccg-tagCTGAGCCACTACGAGAAGGAGCTGGAGGAGATGAAGCACATGTCGAGGCAGGAGTTCATTGCACACCTGAGAAG

upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G091527_T01 (Zea mays), 3'ss of exon 3
gtaagtcatgaatcgtgtgccgtcatgtcattctgccgctaattaatgtgtccacaagtattctgagcttgacgccaaggcatgtggcgagcgtgatgctctgagcttagca-gttctgaggaacggtgcctcatgcacgtggaatggtggaatgttgtgcgacagCTTGGTACATATGAAAAAGAGCTGGAGGAGATGAAGAACATGTCTCGGCAGGAGTATGTGGCCTCGTTGAGGAG
                                                            | | |    ||| ||    | |     ||| |||     ||||| | | | | | | || | |  | ||    ||    |   |  |   |  ||  |     ||| | |     ||     |  ||||||||||||||||||||||| |  |||||||||| || ||     |||| ||
------------------------------------------------------------tcccggtaatga-gctgctgaacacaacgatcgt--ctgtctgaacatggtatggtgtgtgtactgctgatagatctttgcaca-cgtctgtttgccgatt--cagGTCGAGGACTACAGGGAGCAGCTGGAGGAGATGAAGAACATGACCAGGCAGGAGTACGTCGCTCACCTGAGAAG

upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ21317 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtcatgaatcgtgtgccgtcatgtcattctgccgctaattaatgtgtccacaagtattctgagcttgacgccaaggcatgtggcgagcgtgatgctctgagcttagcagttctgaggaacggtgcctcatgcacgtg-gaatggtggaatgttgtgcgacagCTTGGTACATATGAAAAAGAGCTGGAGGAGATGAAGAACATGTCTCGGCAGGAGTATGTGGCCTCGTTGAGGAG
                                                                                          | | ||| |  |   ||| | | |  | | ||||  |  |     |  |||  ||    |   || |  ||  |||||  ||   |||||||| ||||| |||||||||||  ||||| | |||||||||| |||||| ||  | || ||
------------------------------------------------------------------------------------------gtgagattccttcctctt-gtattattcatgaac--tcacaagaccgtgtgtaaactacgttttgattggcatcagCTAAGTGACTATGAAAAGGAGCTAGAGGAGATGAAACACATGACACGGCAGGAGTTTGTGGCTTCCCTTAGAAG

upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtcatgaatcgtgtgccgtcatgtcattctgccgctaattaatgtgtccacaagtattctgagcttgacgccaaggcatgtggcgagcgtgatgctctgagcttagcagttctgaggaacggtgcctcatgcacgtg-gaatggtggaatgttgtgcgacagCTTGGTACATATGAAAAAGAGCTGGAGGAGATGAAGAACATGTCTCGGCAGGAGTATGTGGCCTCGTTGAGGAG
                                                                                          |   ||| |  |   ||| | | |  | | ||||  |  |     |  |||  ||    |   || |  ||  |||||  ||   |||||||| |||||||||||||||||  ||||| | |||||||||| |||||| ||  | || ||
------------------------------------------------------------------------------------------gtaagattccttcctctt-gtattattcatgaac--tcacaagaccgtgtgtaaactacgttttggttggcatcagCTAAGTGACTATGAAAAGGAGCTGGAGGAGATGAAACACATGACACGGCAGGAGTTTGTGGCTTCCCTTAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcatgaatcgtgtgccgtcatgtcattctgccgctaattaatgtgtccacaagtattctgagcttgacgccaaggcatgtggcgagcgtgatgctctgagcttagcagttctgaggaacggtgcctcatgcacgtggaatggtggaatgttgtgcgacagCTTGGTACATATGAAAAAGAGCTGGAGGAGATGAAGAACATGTCTCGGCAGGAGTATGTGGCCTCGTTGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG