Sequence
atgc intronic sequence ATGC exonic sequencegttcaacgcaccttcactctcgatcttatctatatgctgtatgatggttgcacacattagaggttacgattttctataaggttccagtgacacattcaaagtgggtatggccaacagATGGACAGAGCCTCCATACTCGGTGACGCAATTGAGTACCTGAAGGAGCTCCTACAGCGCATCAACGACATTCACAACGAGCTGGAAGAAGCAAAGTTGG
Basic information
species | Physcomitrella patens |
transcript | PP1S257_22V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S257_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os01g70310.1 (Oryza sativa), 3'ss of exon 2
gttcaacgcaccttcactctcgatcttatctatatgctgtatgatggttgcacacattagaggttacgattttc--tataaggttccagtgacacattcaaagtgggtatggccaacagATGGACAGAGCCTCCATACTCGGTGACGCAATTGAGTACCTGAAGGAGCTCCTACAGCGCATCAACGACATTCACAACGAGCTGGAAGAAGCAA--AGTTGG
| | | || | | ||| |||| | ||| || || | || | |||| || | | || | || | || || | | ||||||||||||||| || || || ||||| |||||||||||| ||||||||||||| ||| | || ||||| ||||||| || || || || || |
-------------tta-tgtcaaagtgttcttaatgcca-actatgtctg-actcgtttcatgttaatatctatagtttatcatctcattaccagttttcttct---cctttgtgacagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT--
upper sequence: PP1S257_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os11g32100.1 (Oryza sativa), 3'ss of exon 1
gttcaacgcaccttcactctcgatcttatctatatgctgtatgatggttgcacacattagaggttacgattttctataaggttccagtgacac-attcaaagtgggtatggccaacagATGGACAGAGCCTCCATACTCGGTGACGCAATTGAGTACCTGAAGGAGCTCCTACAGCGCATCAACGACATTCACAACGAGCTGGAAGAAGCAAAGTTGG
||| || | || ||||| | || | | | | ||| | || || | | || | | | ||| | ||| | |||||||||| || ||||| ||||| ||||| |||||||||||||||||||| || ||| ||||| || |||| || ||||| || | |
------------ggtactactaatatcattcatatg----aaagcaattctata-gtgatgcattat-acttgtgatgatttagcaataagatgattatatgtgtttgcaattggtagATGGACAGGGCTTCCATTCTCGGCGACGCGATTGAGTACCTGAAGGAGCTGCTGCAGAAGATCAATGATCTTCAGAATGAGCTCGAGTCGTCCCCCGCGA
upper sequence: PP1S257_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G033356_T01 (Zea mays), 3'ss of exon 1
gttcaacgcaccttcactctcgatcttatc--tatatgctgtatgatggttgcacacattagaggttacgattttctataaggttccagtgacacattcaaagtgggtatggccaac----agATGGACAGAGCCTCCATACTCGGTGACGCAATTGAGTACCTGAAGGAGCTCCTACAGCGCATCAACGACATTCACAACGAGCTGGAAGAAGCAAAGTTGG
|||||| || || || || || | | || | || || | | | | || | | | || | | | |||| |||||||||| |||||||| ||||| |||||||| ||||||||||||||||| || ||| |||||||| |||| || || ||||| | |
-----------------------tcttattggtacatacttcattatattgataggtatcactagtgttacttcctccttttgaccgggcaacgaactgattgtttctgttggcaactggtagATGGACAGGGCCTCCATTCTCGGCGACGCAATCGAGTACCTGAAGGAGCTGCTGCAGAAGATCAACGATCTTCAGAATGATCTGGAGTCGTCCCCTTCCA
upper sequence: PP1S257_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G172297_T01 (Zea mays), 3'ss of exon 1
gttcaacgcaccttcactctcgatcttatctatatgctgtatgatggttgcacacattagaggttacgattttctataaggttccagtgacacattcaaagtgggtatggccaacagATGGACAGAGCCTCCATACTCGGTGACGCAATTGAGTACCTGAAGGAGCTCCTACAGCGCATCAACGACATTCACAACGAGCTGGAAGAAGCAAAGTTGG
| | || | || || | | | || ||| | | | | ||| | || || || || | || | |||||||||| |||||||| ||||| ||||| || ||||||||||||||||| || | | ||| | || | || |||||| |||| | || |
-------------gttcccatagaattgtagatgccct-tgttgtctctgactgcatccttcactgcattcatagatatcactagtgtaactttctctggctgtttctgt---aaagATGGACAGGGCCTCCATTCTCGGCGACGCGATCGAGTACCTGAAGGAGCTGCTGCGGAAGATCGAGGAGCTCCAGAACGAGGTGGAGTCATCAGCATCCC
upper sequence: PP1S257_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G173534_T02 (Zea mays), 3'ss of exon 1
gttcaacgcaccttcactctcgatcttatctatatgctgtatgatggttgcacacattagaggtta--cgattttct---ataaggttccagtgacacattcaaagtgggtatggc-caacagATGGACAGAGCCTCCATACTCGGTGACGCAATTGAGTACCTGAAGGAGCTCCTACAGCGCATCAACGACATTCACAACGAGCTGGAAGAAGCA--AAGTTGG
| | | ||| ||| | | ||| || | ||| | | || || ||| | | | || || | || ||||||||| || || || || || || |||||||||||||| |||||||||||||| ||| | |||| ||| ||||||| || || || ||| || |
-----------------------acacgcttggacgcttcgccatgatagtacatgtttggtattaatcaacttgctttagtaaatgttgattctcatcagcatttctcttctgctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT--
upper sequence: PP1S257_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ29742 (Selaginella moellendorffii), 3'ss of exon 1
----gttcaacgcaccttcactctcgatct--tatctatatgctgtatgatggttgcacacattagaggttacgattttctataaggttccagtgacacattcaaagtgggtatggccaa-cagATGGACAGAGCCTCCATACTCGGTGACGCAATTGAGTACCTGAAGGAGCTCCTACAGCGCATCAACGACATTCACAACGAGCTGGAAGAAGCAA-AGTTGG
|| | | | | | | | | || | || | | || || | || | || || | | || | |||| |||| ||| | |||||||| ||||| || || || |||||||| || ||||| || ||||||||||| ||| | |||||||| | |||| ||||||||||| || || ||
gtgagtactttcaaaccactcgggcaacttggcattcactcgcccgctcctctttccatgcctttacctcttt--ttctcctctcgctctcact--cacactcaacttggtttgattttgtcagATGGATAGAGCATCTATTCTGGGTGACGCGATCGAGTATCTCAAGGAGCTCCTCCAGAGGATCAACGAGCTCCACAGCGAGCTGGAAGGCCCAGCAGATG-
upper sequence: PP1S257_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ28242 (Selaginella moellendorffii), 3'ss of exon 1
gttcaacgcaccttca---ctctcgatcttatctatatgctgtatgatggttgcacacatta-gaggttacgattttctataaggttccagtgacacattca-aagtgggtatggcc--aacagATGGACAGAGCCTCCATACTCGGTGACGCAATTGAGTACCTGAAGGAGCTCCTACAGCGCATCAACGACATTCACAACGAGCTGGAAGAAGCAA-AGTTGG
| || |||| | |||| | | || | | | | | | | | | |||| ||| | | | | | || || || || | ||| || |||||||| ||||| || || || |||||||| || ||||| || ||||||||||| ||| | |||||||| | |||| ||||||||||| || || ||
---gtgagtactttcaaaccactcgggcaacttggcattcact-cgcccgctcctctttccatgcctttacctctttttctcctctcgctctcactcactctcaacttggtttgattttgtcagATGGATAGAGCGTCTATTCTGGGTGACGCGATCGAGTATCTCAAGGAGCTCCTCCAGAGGATCAACGAGCTCCACAGCGAGCTGGAAGGCCCAGCAGATG- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttacgattttctataaggttccagtgacacattcaaagtgggtatggccaacagATGGACAGAGCCTCCATACTCGGTGACGCAATTGAGTACCTGAAGGAGCTCCTACAGCGCATCAACGACATTCACAACGAGCTGGAAGAAGCAAAGTTGG
attttctataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcaacgcaccttcactctcgatcttatctatatgctgtatgatggttgcacacattagaggttacgattttctataaggttccagtgacacattcaaagtgggtatggccaacagATGGACAGAGCCTCCATACTCGGTGACGCAATTGAGTACCTGAAGGAGCTCCTACAGCGCATCAACGACATTCACAACGAGCTGGAAGAAGCAAAGTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG