Sequence
atgc intronic sequence ATGC exonic sequence...ttttcagacgtagcattaaagtttcgaccagtctctagtgggccacagtattcgtttcgacgcttaagtttgttaatgaaaatttggttctttattatagATACGATGCTCACTCCGGTGGAGAACGAGAAATTCAGCGGACTATGTTGGAGTTGTTGAATCAGTTGGATGGATTTGATGCTCGTGGTGACGTAAAAGTC
Basic information
species | Physcomitrella patens |
transcript | PP1S109_234V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 3
------------------------------ttttcagacgtagcattaaagtttcgaccagtctctagtgggccacagtattcgtttcgacgcttaagt--ttgttaatgaaaatttggttcttta-ttatagATACGATGCTCACTCCGGTGGAGAACGAGAAATTCAGCGGACTATGTTGGAGTTGTTGAATCAGTTGGATGGATTTGATGCTCGTGGTGACGTAAAAGTC
|| | | | | || || | ||| | || | | | | | ||| | | || ||||| ||| || | | |||||| || |||||||| || |||||||| || ||||||||| | || |||||||||||| | |||||| ||||||| |||||| | | || || || |||||
gtagagtagtgcatacttcaaatgggaagtcttctatatgatgaatgttgtttgtgtatagtaaaagattggtggaacttcccatgaaatagtttatatgagtattgatgaacttttttttttctccttatagGTATGATGCTCATTCGGGTGGAGAGCGTGAAATTCAGAGAACCATGTTGGAGTTGCTTAATCAGCTGGATGGTTTTGATTCAAGGGGAGATGTTAAAGTT
upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 3
----ttttcagacgtagcattaaagtttcgaccagtctctagtgggccacagtattcgtttcgacgcttaagtttgttaatgaaaatttggttctttattatagATACGATGCTCACTCCGGTGGAGAACGAGAAATTCAGCGGACTATGTTGGAGTTGTTGAATCAGTTGGATGGATTTGATGCTCGTGGTGACGTAAAAGTC
||| | | || | | ||| | | || | | || | | | | |||| | | || ||| | | || ||| || |||||||| || ||||| || || || |||||| | || |||||||||||||| |||||| ||||||| |||||| | | || || || |||||
ggtctttcccttcccggc--tgagatttttatgaaaaaaatgttg-ctgaagcttctagtgaaaggattaatatgagttttgctg-tttctcgccctgttgtagGTATGATGCTCATTCTGGTGGTGAGCGTGAGATTCAGAGAACCATGTTGGAGTTGTTAAATCAGCTGGATGGTTTTGATTCAAGAGGAGATGTTAAAGTT
upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------ttttcagacgtagcatt----aaagtttcgaccagtctctagtgggccacagtattcgtttcgacgcttaagtttgttaatgaaaatttggttc-tttattatagATACGATGCTCACTCCGGTGGAGAACGAGAAATTCAGCGGACTATGTTGGAGTTGTTGAATCAGTTGGATGGATTTGATGCTCGTGGTGACGTAAAAGTC
||||| || | || | | | | || | || | | | || | | || || ||| | | | | || | ||| || || ||||| ||||| ||||||||||| ||||||||| ||||||||||||||||| |||| ||||| ||||| |||||| | | || |||||||||||
gtaagttattgaacatcagctttaggagtcactgtgtcaagacattttctatcttcttttttctgatttttttttccgggagggggcaggggatgcgggactggttatag-agtgatatcatggatcaa--ttcttagtatatgtctcttttatgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGACGTAAAAGTT
upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------ttttcagacgtagcattaaagtttcga-----ccagtctctagtgggcc---acagtattcgtttcgacgcttaagtttgttaatgaaaatttggttctttattatagATACGATGCTCACTCCGGTGGAGAACGAGAAATTCAGCGGACTATGTTGGAGTTGTTGAATCAGTTGGATGGATTTGATGCTCGTGGTGACGTAAAAGTC
||| | || |||| || ||| | ||| || || | | | | | | || | || | | | || | | | | || || || ||||| ||||| ||||||||||| ||||||||| ||||||||||||||||| |||| ||||| ||||| || ||| | | ||||| || |||||
gtaagttatcgagtatcagcttctggagtcactgttttaagacattttctatcctctttttccggatgtagttttttgttttgggaggaggcagggggtacaggactggtagaagagtgatatcatgagtcaattcttattatatgtctcttatatgct-ttgcagGTATGATGCCCACTCAGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTCGATTCAAGAGGTGATGTTAAAGTG
upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 3
------------------------------------ttttcagacgtagcattaaagtttcg-accagtctctagtgggccacagtattcgtttc---gacgcttaagtttgttaatgaaaatttggttctttattatagATACGATGCTCACTCCGGTGGAGAACGAGAAATTCAGCGGACTATGTTGGAGTTGTTGAATCAGTTGGATGGATTTGATGCTCGTGGTGACGTAAAAGTC
|| | | | | | | | | | || ||||| | | | |||| |||| | | | || || | | || || | || | || || ||||||||||| ||||||||||| || ||||| |||| ||||| |||||| |||| ||||| ||||| |||||| || | || || ||||||||
gtaattttaacccccaactttagctgtcatgaaggtaccggggatggaagagtgatgccttgtatca--ctctatgagctcttgggattcttttcctacattcatgagcttaccagtaaatatgtattt-------acagGTATGATGCTCACTCAGGTGGAGAACGTGAGATTCAAAGGACCATGTTAGAGTTGCTGAACCAGTTAGATGGTTTTGATTCTAGAGGAGATGTAAAAGTG
upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 3
--------------------------------------ttttcagacgtagcattaaagtttcg-accagtctctagtgggccacagtattcgtttcg---acgcttaagtttgttaatgaaaatttggttctttattatagATACGATGCTCACTCCGGTGGAGAACGAGAAATTCAGCGGACTATGTTGGAGTTGTTGAATCAGTTGGATGGATTTGATGCTCGTGGTGACGTAAAAGTC
| | | | | | | || | | | || ||||| | | || |||| |||| | | | || || |||| || || | || | || || ||||||||||| || |||||||| |||||||| |||| ||| | |||||| |||| ||||| ||||| |||||| | | || || || |||||
gtaattttaacctccaactttagtattcatgaaggtagggtggggttggaagagtgatgtcttgtatca--ctctatgagctcttaggattcttttcctacattcatgagcttactaataaatatgtattt-------acagGTATGATGCTCACTCAGGAGGAGAACGTGAAATTCAAAGGACCATGCTAGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGATGTGAAAGTG
upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 3
ttttcagacgtagcattaaagtttcgaccagtctctagtgggccacagtattcgtttcgacgcttaagt-ttgttaatgaaaatttggttctttattat--agATACGATGCTCACTCCGGTGGAGAACGAGAAATTCAGCGGACTATGTTGGAGTTGTTGAATCAGTTGGATGGATTTGATGCTCGTGGTGACGTAAAAGTC
| ||||| || | | ||| | |||| || | || | || || ||||| ||||| |||||||| || |||||||||||||| ||| | ||| || |||| ||| | ||||| || |||||||| |||||||| |||||
--------------------------------------------------gtgatttcgttgcatggttgttgcagaaactaattgggaacaaccttctcaagGTATGATGCACACTCTGGTGGAGAGCGCGAAATTCAGCGGACCATGCTTGAGCTGCTGAACCAGCTCGATGGTTTCGATGCTCGGGGTGACGTGAAAGTT
upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 3
ttttcagacgtagcattaaagtttcgaccagtctctagtgggccacagtattcgtttcgacgcttaagt-ttgttaatgaaaatttggttc--tttattatagATACGATGCTCACTCCGGTGGAGAACGAGAAATTCAGCGGACTATGTTGGAGTTGTTGAATCAGTTGGATGGATTTGATGCTCGTGGTGACGTAAAAGTC
| ||||| | | | ||| | |||| || | | | ||| || ||||| ||||| |||||||| || |||||||||||||| ||| | ||| || |||| ||| | ||||| || |||||||| |||||||| |||||
--------------------------------------------------gtgatttcgttacatggttgttgcagaaactaattgggaacaaccttctctagGTATGATGCACACTCTGGTGGAGAGCGCGAAATTCAGCGGACCATGCTTGAGCTGCTGAACCAGCTCGATGGTTTCGATGCTCGGGGTGACGTGAAAGTTMapped 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|67694035|gb|BJ954268.1|BJ954268EST: TCTCCTACCATCGTCTTTATTGACGAAATTGATGCCGTCGGTACGAAGAG ATACGATGCTCACTCCGGTGGAGAACGAGAAATTCAGCGGACTATGTTGGA
genomic: TCTCCTACCATCGTCTTTATTGACGAAATTGATGCCGTCGGTACGAAGAGgtaattcccg ... tttattatagATACGATGCTCACTCCGGTGGAGAACGAGAAATTCAGCGGACTATGTTGGA
EST:
gi|162197603|gb|FC374437.1|FC374437EST: TCTCCTACCATCGTCTTTATTGACGAAATTGATGCCGTCGGTACGAAGAG ATACGATGCTCACTCCGGTGGAGAACGAGAAATTCAGCGGACTATGTTGGA
genomic: TCTCCTACCATCGTCTTTATTGACGAAATTGATGCCGTCGGTACGAAGAGgtaattcccg ... tttattatagATACGATGCTCACTCCGGTGGAGAACGAGAAATTCAGCGGACTATGTTGGA
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:
31 (upstream exon),
12 (downstream exon)
Score:
3GTGATGGACCAAAGTTGGTACGAGAGTTGTTTCGGGTTGCAGACGAATTGTCTCCTACCATCGTCTTTATTGACGAAATTGATGCCGTCGGTACGAAGAGgtaattcccg ... tttattatagATACGATGCTCACTCCGGTGGAGAACGAGAAATTCAGCGGACTATGTTGGAGTTGTTGAATCAGTTGGATGGATTTGATGCTCGTGGTGACGTAAAAGTC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagtattcgtttcgacgcttaagtttgttaatgaaaatttggttctttattatagATACGATGCTCACTCCGGTGGAGAACGAGAAATTCAGCGGACTATGTTGGAGTTGTTGAATCAGTTGGATGGATTTGATGCTCGTGGTGACGTAAAAGTC
tgttaat putative branch site (score: 3)
ttctttatt putative PPT
ttaatgaaaatttggt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttcagacgtagcattaaagtttcgaccagtctctagtgggccacagtattcgtttcgacgcttaagtttgttaatgaaaatttggttctttattatagATACGATGCTCACTCCGGTGGAGAACGAGAAATTCAGCGGACTATGTTGGAGTTGTTGAATCAGTTGGATGGATTTGATGCTCGTGGTGACGTAAAAGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA