Sequence
atgc intronic sequence ATGC exonic sequencegtacataattatgtatacatagcttgatgtgcattctattattctgcattcgatatgcagtaggtgcttatggatttattttcttcatgaacatcctcgtaaattcttttcttattacagcttttctccgttcacaagcttacatgtttttgttgtttgtaactgcagGTGTGCATGATTCATACTGGACACATGCAGGTGACGTAGAGCAAATGAACAGCCTGCTCCGTGAGAAGTTTGTTGAACTCTACAGTCAACCAGTTTTGGA
Basic information
species | Physcomitrella patens |
transcript | PP1S256_41V6.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S256_41V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: GLYMA08G32320.6 (Glycine max), 3'ss of exon 9
gtacataattatgtatacatagcttgatgtgcattctattattctgcattcg-atatgcagtaggtgcttatggatttattttcttcatgaacatcctcgtaaattcttttcttattacagcttttctccgttcacaagcttacatgtttttgttg-tttgtaactgcagGTGTGCATGATTCATACTGGACACATGCAGGTGACGTAGAGCAAATGAACAGCCTGCTCCGTGAGAAGTTTGTTGAACTCTACAGTCAACCAGTTTTGGA
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--------------------------gtgcttattggtttatataacacgcacatatacagt---catatgtgaatgaaatttgtttgtg----ctcttgtta------tgtacatcaatgttgacttttgattaggaatttaaatttgtaaatcgatgcttaaatgcagGGGTTCATGATTCATATTGGACACATGCGTGTGATGTTGATGAAATGAACAGGATACTCAGGGAAAAGTTTGTTGAACTCTATGATGCTCCAATATTGGA
upper sequence: PP1S256_41V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: AT2G24120.1 (Arabidopsis thaliana), 3'ss of exon 17
gtacataattatgtatacatagcttgatgtgcattctattattctgcattcgatatgcagtaggtgcttatggatttattttcttcatgaacatcctcgtaaattcttttcttattacagcttttctccgttcacaagcttac-atgtttttgttg-----tttgtaactgcagGTGTGCATGATTCATACTGGACACATGCAGGTGACGTAGAGCAAATGAACAGCCTGCTCCGTGAGAAGTTTGTTGAACTCTACAGTCAACCAGTTTTGGA
| || || ||| | | || | | | | | || || || || ||| || | |||||||||||||||| ||||||||||| |||||| ||||||| || ||||||||| | || | ||||| || ||||| || |||| ||| | | ||
----------------------------------------------------------------------------------------------gttagttctgtcaattcgactaatggcctaccaacaaaaaaagaagtattatcttcttattgaatgcttgggttctgcagGTGTGCATGACTCATACTGGACCCATGCATGTGACGTTGACACAATGAACAGAATACTTAGAGAGAAATTCGTTGAGCTTTACAACACACCGATCCTTGA
upper sequence: PP1S256_41V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: Vv01s0010g00690.t01 (Vitis vinifera), 3'ss of exon 17
gtacataattatgtatacatagcttgatgtgcattctattattctgcattcgatatgcagtaggtgcttatggatttattttcttcatgaacatcctcgta-aattcttttcttattacagcttttctccgttcacaagcttacatgtttttgttgtttgtaactgcagGTGTGCATGATTCATACTGGACACATGCAGGTGACGTAGAGCAAATGAACAGCCTGCTCCGTGAGAAGTTTGTTGAACTCTACAGTCAACCAGTTTTGGA
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---------------------gttttgtagatactttccttgtacccattttctgctgattaaaa---cacagataaatt-----catgtacactcacatataatatacatactatttgtgttttgtttttcttactgttctgcac-----caatgtttg--gtcacagGAGTCCATGATTCATACTGGACACATGCATGTGATGTTGACGAAATGAACAGGATACTTAGAGAAAAGTTTGTTGAACTCTACGGGATGCCAATACTTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attacagcttttctccgttcacaagcttacatgtttttgttgtttgtaactgcagGTGTGCATGATTCATACTGGACACATGCAGGTGACGTAGAGCAAATGAACAGCCTGCTCCGTGAGAAGTTTGTTGAACTCTACAGTCAACCAGTTTTGGA
ttgtaac putative branch site (score: 2)
atgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacataattatgtatacatagcttgatgtgcattctattattctgcattcgatatgcagtaggtgcttatggatttattttcttcatgaacatcctcgtaaattcttttcttattacagcttttctccgttcacaagcttacatgtttttgttgtttgtaactgcagGTGTGCATGATTCATACTGGACACATGCAGGTGACGTAGAGCAAATGAACAGCCTGCTCCGTGAGAAGTTTGTTGAACTCTACAGTCAACCAGTTTTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT