Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaatatttttcattgtgtgatacttgttcaaaaatatttatttcttgcatgcacttttgagtgatggttcgactaacattttacattgtttgcttcgatgctctgtagGCTGTTATTGATGCCAACATCATTCCACCTTTGGTATCTCTTCTTGCCACCGCAGAATTTGACATCAAGAAGGAAGCTGCTTGGGCTATTTCAAATGCCA
Basic information
species | Physcomitrella patens |
transcript | PP1S165_54V6.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S165_54V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os05g06350.1 (Oryza sativa), 3'ss of exon 8
gtaaaaatatttttcattgtgtgatacttgttcaaaaatatttatttcttgcatgcacttttgagtgatggttcgactaacattttacattgtttgcttcgatgctctgtagGCTGTTATTGATGCCAACATCATTCCACCTTTGGTATCTCTTCTTGCCACCGCAGAATTTGACATCAAGAAGGAAGCTGCTTGGGCTATTTCAAATGCCA
|| | || || || | || | || | || | | |||| || || |||| | ||| ||||||| || |||| ||||| ||| | ||| | ||| ||| || || || ||||||||||||||||| || ||||| ||||| || ||||||||||
--------------------gttggtgtgatttgaagctag--aattatcatattgatatt--gcttacaacattgctaaaatacta--ttgtccg---------tctacagGCTGTGATCAATGCAAACATAATTGCTCCTCTAGTACATCTGCTGCAAACTGCTGAATTTGACATCAAGAAAGAGGCTGCGTGGGCAATCTCAAATGCCA
upper sequence: PP1S165_54V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G088088_T01 (Zea mays), 3'ss of exon 8
gtaaaaatatttttcattgtgtgatacttgttcaaaaatatttatttcttgcatgcacttttgagtgatggttcgactaacattttacattgtttgcttcgatgctctgtagGCTGTTATTGATGCCAACATCATTCCACCTTTGGTATCTCTTCTTGCCACCGCAGAATTTGACATCAAGAAGGAAGCTGCTTGGGCTATTTCAAATGCCA
| ||||| | ||||| |||| | || || || || | | || | ||| | | ||| | || ||||||| || |||| || || ||| ||||| |||| || || || || ||||||||||||||||| ||||| || ||||| |||||||||||||
------acattttctcccagtcccagcaacttcaatgatatca----cctggttggtctcttattcaactgctccgttc-tgtttggtttcttcccaaattatggt-tgcagGCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACTGCTGAATTTGACATCAAGAAAGAAGCAGCCTGGGCAATTTCAAATGCCA
upper sequence: PP1S165_54V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G009845_T02 (Zea mays), 3'ss of exon 8
gtaaaaatatttttcattgtgtgatacttgttcaaaaatatttatttcttgcatgcacttttgagtgatggttcgactaacattttacattgtttgcttcgatgctctgtagGCTGTTATTGATGCCAACATCATTCCACCTTTGGTATCTCTTCTTGCCACCGCAGAATTTGACATCAAGAAGGAAGCTGCTTGGGCTATTTCAAATGCCA
| ||| | ||| ||| | || || | | ||| || || ||||| | | || ||| || ||| ||| |||| || ||| |||| ||||| ||| ||||| |||| ||||| || || ||||||||||||||||| ||||| || ||||| |||||||||||||
---ttggtttttcttattcaactccactctgtttggttggcttcttattcaactccaccattctgtt-tggttt------cttcctaaattactt--ttcatatggctgcagGCCGTGATTAATGCAAACATAATTGCACCTCTGGTGCAACTTCTGCAAACTGCTGAATTTGACATCAAGAAAGAAGCAGCCTGGGCAATTTCAAATGCCA
upper sequence: PP1S165_54V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 8
gtaaaaatatttttcattgtgtgatacttgttcaaaa-atatttatttcttgcatgcacttttgag-tgatggttcgactaacattttacattgtttgcttcgatgctctgtagGCTGTTATTGATGCCAACATCATTCCACCTTTGGTATCTCTTCTTGCCACCGCAGAATTTGACATCAAGAAGGAAGCTGCTTGGGCTATTTCAAATGCCA
| | || || | | ||| || ||| | || || ||| | |||| | | || | || | | | | | ||| | || || | |||||||| || |||| ||||| | |||||| | || ||| || ||||| ||||| ||||||||||| ||||||||||| || |||||||| |
--------actattaataattt-atattttctcactacatgcttctttgcttcatgtgttcaaaaaatgttagt--aattgattactcgctttgctgtactcaatttt---tagGCTGTCATAAGTGCCGGTATCATCGCTCCTTTGTTGCAACTGCTTCAAACAGCAGAGTTTGATATCAAGAAGGAGGCTGCTTGGGCCATCTCAAATGCTA
upper sequence: PP1S165_54V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA20G38320.2 (Glycine max), 3'ss of exon 8
gtaaaaatattt-ttcattgtgtgatacttgttcaaaaatatttatttcttgcatgcacttttgagtgatggttcgactaacattttacattgtttgcttcgatgctctgtagGCTGTTATTGATGCCAACATCATTCCACCTTTGGTATCTCTTCTTGCCACCGCAGAATTTGACATCAAGAAGGAAGCTGCTTGGGCTATTTCAAATGCCA
||| | || || |||||| | || || || || || || | | ||| ||| | || | ||| ||||| | | || || ||| | ||||||| ||||| || || | ||| | |||||||| ||| ||| | || || ||||| |||||||| ||||||||||||||||| |||||||| |
gtatagttacttgttcattttatggtaatt-------aaggcttgattttcac-----ttttaaagttcttattgcaataatatttt-cttcaattcct--gataataaacagGCTGTGATTGAGGCTAATCTAATTGCTCCTTTGGTCAATCTGCTTCAAAATGCTGAGTTTGATATCAAGAAAGAAGCTGCTTGGGCTATCTCAAATGCTA
upper sequence: PP1S165_54V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA10G29000.1 (Glycine max), 3'ss of exon 8
gtaaaaatatttttcattgtgtgatacttgttcaaaaatatttatttcttgcatgcacttttgagtgatggttcgactaacattttacattgtttgcttcgatgctctgtagGCTGTTATTGATGCCAACATCATTCCACCTTTGGTATCTCTTCTTGCCACCGCAGAATTTGACATCAAGAAGGAAGCTGCTTGGGCTATTTCAAATGCCA
|| || | ||||| | ||| ||| || | || ||| | || | ||| ||| | | | || || ||| | | ||||||| ||||| || || | ||| | |||||||| ||| ||| | || || ||||| |||||||| ||||||||||||||||| |||||||| |
-------------gtatagttacttgtttgttttatgataattaaacctccattttcacttgaagttcttattgcaataatattct-cttcaattcct--gataataagcagGCTGTGATTGAGGCTAATCTAATTGCTCCTTTGGTCAATCTGCTTCAAAATGCTGAGTTTGATATCAAGAAAGAAGCTGCTTGGGCTATCTCAAATGCTA
upper sequence: PP1S165_54V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA17G03430.1 (Glycine max), 3'ss of exon 8
gtaaaaatatttttcattgtgtgata--cttgttcaaaaatatttatttcttgcatgcacttttgagtgatggttcgactaacattttacattgtttgcttcgatgctctgtagGCTGTTATTGATGCCAACATCATTCCACCTTTGGTATCTCTTCTTGCCACCGCAGAATTTGACATCAAGAAGGAAGCTGCTTGGGCTATTTCAAATGCCA
|| | |||| ||| | ||| |||| | || | | | | || | ||| || ||| || | |||| | | ||||||| |||||||||| || | || |||| | || ||||||| | || ||||||||||| || ||||||||||||||||| || |||||||| |
----cgatttgaatcatgaattgacaaccttattcatattaatgcaaagtgtaagatttttcctttttgtttgttagaaaaac-ttatgcattctata---------tctgtagACTGTTATTGAAGCTGGTCTGGTTGCACCCCTTGTCAATCTTCTTCAAAATGCGGAATTTGACATTAAAAAGGAAGCTGCTTGGGCAATCTCAAATGCTA
upper sequence: PP1S165_54V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT3G06720.2 (Arabidopsis thaliana), 3'ss of exon 8
gtaaaaatatttttcattgtgtgat-acttgttcaaaaatatttatttcttgcatgcacttttgagtgatggttcgactaacattttacattgtttgcttcgatgctctgtagGCTGTTATTGATGCCAACATCATTCCACCTTTGGTATCTCTTCTTGCCACCGCAGAATTTGACATCAAGAAGGAAGCTGCTTGGGCTATTTCAAATGCCA
| | || | ||| | || | |||| | |||| |||| | | ||| | ||| || | | ||| | |||| | || || | || |||| || || | ||| | || ||||| ||| ||| | || ||||||||||| |||||||||||||| ||||| ||||||||||| |
--gtaggcaattagtactgtttcatcatatgttttgta----ccgtttcccatccagacttcta--tacctattc-attaa--ttgtgttgtttttcccctgatggt-tgcagACGGTAGTTGAGGCTAATTTGATTTCCCCGTTGGTGAGTCTGCTTCAAAATGCTGAATTTGACATTAAGAAGGAAGCTGCATGGGCAATTTCAAATGCAA
upper sequence: PP1S165_54V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv07s0005g01100.t01 (Vitis vinifera), 3'ss of exon 8
gtaaaaatatttttcattgtgtgatacttgttcaaaaatatttatttcttgcatgcacttttgagtgatggttcgactaacattttacattgtttgcttcgatgctctgtagGCTGTTATTGATGCCAACATCATTCCACCTTTGGTATCTCTTCTTGCCACCGCAGAATTTGACATCAAGAAGGAAGCTGCTTGGGCTATTTCAAATGCCA
| || | ||| | | ||| || ||| ||||| ||| | | | ||| | || | | | | | || || || | || || |||| ||||| || ||||||||| || | | | ||| ||| | || |||||||| |||||||| || ||||||||||| ||||||||||| |
----ttgttattattattattatttttttgacttttaaagttttattcttttatgtatctgt---tgagag---gaatgatacta-gtggaatgtgttttgaaa-tatgcagTCTGTAATTGAGGCTGGCATCATTCCTCCCCTTATCTATCTGCTTCAAAATGCTGAATTTGAGATCAAGAAAGAGGCTGCTTGGGCCATTTCAAATGCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttgagtgatggttcgactaacattttacattgtttgcttcgatgctctgtagGCTGTTATTGATGCCAACATCATTCCACCTTTGGTATCTCTTCTTGCCACCGCAGAATTTGACATCAAGAAGGAAGCTGCTTGGGCTATTTCAAATGCCA
gactaac putative branch site (score: 1)
taacattttacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaatatttttcattgtgtgatacttgttcaaaaatatttatttcttgcatgcacttttgagtgatggttcgactaacattttacattgtttgcttcgatgctctgtagGCTGTTATTGATGCCAACATCATTCCACCTTTGGTATCTCTTCTTGCCACCGCAGAATTTGACATCAAGAAGGAAGCTGCTTGGGCTATTTCAAATGCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT