Sequence
atgc intronic sequence ATGC exonic sequence...tgtttcgcatgcatccccagttgatcattccacatcccccaagcggattcttcattacaataatcgctgttctgaatgtcctcgccgtggtgtgctacagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGATCGGCATTACCAAGTCCGAAGACAACGGCATTCATCTGACGTTCGATCACCCGACTCAGCCAGGTA
Basic information
species | Physcomitrella patens |
transcript | PP1S79_76V6.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S79_76V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 3
tgtttcgcatgcatccccagttgatcattccacatcccccaagcggattc--ttcattacaataat--cgctgttctgaatgtcctcgccgtg-gtgtgc-tacagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGATCGGCATTACCAAGTCCGAAGACAACGGCATTCATCTGACGTTCGATCACCCGACTCAGCCAGGTA
| | || | || | | | | | | | | || ||| | || ||| || | | |||| | ||| | ||||| ||||||||||||||||||||| ||||||||| | || | | | | | || ||| |||||| |||||||| ||||| || |
--------------------gtaagcactaagcaccagcaacggcaacgccatccgtttcaacgacgacgatgtgcttacgttttggttcgtgtgcgtgtgtgcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
upper sequence: PP1S79_76V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM5G878558_T01 (Zea mays), 3'ss of exon 3
---------tgtttcg-catgcatcc---ccagttgatcattccacatcccccaagcggattcttcattacaataatcgctgttctgaatgtcctcgccgtggtgtgctacagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGATCGGCATTACCAAGTCCGAAGACAACGGCATTCATCTGACGTTCGATCACCCGACTCAGCCAGGTA
| | | | || ||| || || || | | || ||| || | || ||| ||| | | ||| || | || |||| ||||||||||||||||||||||||||||||||| | | | | | | || || || |||||| |||||| | ||||| || |
gtgagttgccgctccatcgtgtttcccttcccgtggaaccatgcatgtcctcctctccacgactgtgttagcttaaatacacgcacgtgcgtctgttcctctacgcgc---agGGCATGATGAACAACTGCTGGTTCCGGGTGAAGATCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCATGGTGTTCGAGCACCCGGCGCAGCCGGGCA
upper sequence: PP1S79_76V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G428027_T01 (Zea mays), 3'ss of exon 3
------------------------tgtttcgcatgcatccccagttgatcattccacatcccccaagcggattcttcattacaataatcgc-tgttctgaatgtcctcgccgtggtgtgctacagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGATCGGCATTACCAAGTCCGAAGACAACGGCATTCATCTGACGTTCGATCACCCGACTCAGCCAGGTA
|||| || | | | || | || ||| | | || ||| | ||| || || | ||||| || | | || ||||| |||||||||||||||||||||||||||||| || | | | | | | || || ||| |||||| |||||||| ||||| || |
gtgagttaccgcttcatcgtgcttcctttccggtggcttcgccgtcggtccgtccgatgcttgtcttccacggctgtgttagattaaatgcacgtgtggcttgtccgttcctgcgcgcgc-gcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGGTCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
upper sequence: PP1S79_76V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G568636_T01 (Zea mays), 3'ss of exon 3
tgtttcgcatgcatccccagttgatcattccacatcccccaagcggattcttcattacaataatcgctgttctgaatgtcctcgccgtggtg-tgctacagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGATCGGCATTACCAAGTCCGAAGACAACGGCATTCATCTGACGTTCGATCACCCGACTCAGCCAGGTA
| | || | | | ||| | | | || | || | | || | | | || || || || |||||| ||||||||||||||||||||| ||||||| | | | | | | | || || ||| |||||| |||||||| ||||| || |
------gtacatatatatactagcacataatattaatactgaataagtttct-gtttctgctcctgatgatatataaatc-------tgatgatggcacagGGGATGATGAACAACTGCTGGTTCAAGGTGAAGGTGAACGTGTGCCGTCCGCACAAGGGCGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCCGGCA
upper sequence: PP1S79_76V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA14G33480.1 (Glycine max), 3'ss of exon 3
tgtttcgcatgcatccccagttgatcattccacatcccccaagcggattcttcattacaataatcgctgttctga-atgtcctcgccgtggtgtgctac--agGGAATGATGAACAACTGCTGGTTCCGGGTGAAGATCGGCATTACCAAGTCCGAAGACAACGGCATTCATCTGACGTTCGATCACCCGACTCAGCCAGGTA
| || | || | || | || | | | | ||| ||| | || || || |||| | | || | | |||| ||||||||||||||||||||| ||||||| | | ||||| || | | | ||| | ||| || ||||| || || |||| |
---atttcaagggaccaaaaagtattttcccgctttttttcacaagtaaagcaattctaatgaatccttttgtgttatgttttgggaatgcaataatgtgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA
upper sequence: PP1S79_76V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 3
tgtttcgcatgcatccccagttgatcattccacatcccccaagcggattcttcattacaataatcgctgttctgaatgtcctc--------gccgtggtgtgctacagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGATCGGCATTACCAAGTCCGAAGACAACGGCATTCATCTGACGTTCGATCACCCGACTCAGCCAGGTA
| || | ||| | | | | | || | | |||| | || | | || || | | | | | || || ||||||| ||||||||||||||||||||| | ||||| | | | || | || | | | || | | ||| || ||||| || || ||||| |
-------tagcaataaactattgcccgtgacttaaaatctaatcaaaatctttactaaagtgcccgactttgagtctattttattaaataagttttgacatg-tacagGGCATGATGAACAACTGCTGGTTCAGAGTGAAAACCAATGTGTGCAGGCCCCACAAGGGTGAGATAGGTATAGTGTTTGAACACCCCACCCAACCAGGCA
upper sequence: PP1S79_76V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv18s0001g03910.t01 (Vitis vinifera), 3'ss of exon 3
tgtttcgcatgcatccccagttgatcattccacatcccccaagcggattcttc---attacaataatcgctgttctgaat---gtcctcgccgtggtgtgctacagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGATCGGCATTACCAAGTCCGAAGACAACGGCATTCATCTGACGTTCGATCACCCGACTCAGCCAGGTA
||| | | | ||| | | | | | || ||| | || | | |||||| | | | ||| | | ||||||||||||||||||||||||||| | || || | | |||| | | ||| | ||||| || || |||| ||||| |
------tcatagttgcaaacatgagaggcgtgcgtttatgacgtgattttcctataatttccattttgtcgtttctgattagggaaataataatggaattatgcagGGAATGATGAACAACTGCTGGTTCAGAGTAAAAACAAATGTGTGCAAGCGTCACAGGGGAGAGATTGGAATCGTATTCGAGCATCCAACTCTTCCAGGAA
upper sequence: PP1S79_76V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ14822 (Selaginella moellendorffii), 3'ss of exon 4
tgtttcgcatgcatccccagttgatcattccacatcccccaagcggattcttcattacaat-aatcgctgttctgaatgtcctcgccgtggtgtgcta-cagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGATCGGCATTACCAAGTCCGAAGACAACGGCATTCATCTGACGTTCGATCACCCGACTCAGCCAGGTA
||| | |||||| || | | | | || | || | | || | ||||| |||||||||||||||||||||||||||||| || | |||| | | ||| | ||| ||||||| |||||||| | ||| | |
--------------------------------gtgagtggaagtgaattctttggattgatcggtggttctcatggttcgatctctcgggctatggtggcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCGTCCCTGCAAGGGGAAGCTCGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGCCA
upper sequence: PP1S79_76V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ26567 (Selaginella moellendorffii), 3'ss of exon 5
tgtttcgcatgcatccccagttgatcattccacatcccccaagcggattcttcattacaataatcgctgttctgaatgtcctcgccgtggtgtgctacagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGATCGGCATTACCAAGTCCGAAGACAACGGCATTCATCTGACGTTCGATCACCCGACTCAGCCAGGTA
|| | ||| ||| | || || | || | || ||||| ||||| |||||||||||||||||||||||||||||| || |||| | ||| | ||| ||||||| |||||||| | ||| || |
-------------------gtaagtggcagtggatctttgggattgatcggtagttctgatggtt-------cgatctctcgggctatggtg----gcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCATCCCTGCAAGGGGAAGCTGGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattcttcattacaataatcgctgttctgaatgtcctcgccgtggtgtgctacagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGATCGGCATTACCAAGTCCGAAGACAACGGCATTCATCTGACGTTCGATCACCCGACTCAGCCAGGTA
ttcattacaataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtttcgcatgcatccccagttgatcattccacatcccccaagcggattcttcattacaataatcgctgttctgaatgtcctcgccgtggtgtgctacagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGATCGGCATTACCAAGTCCGAAGACAACGGCATTCATCTGACGTTCGATCACCCGACTCAGCCAGGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA