Sequence
atgc intronic sequence ATGC exonic sequencegttcggctatctattccttttgtgcgtgcgctctttgcactgaaccaagcctggtcagtcgtgaatgcgagtactaattggttgttcgaatgttgcagCTAAGCAGCTGTTTCCTACTGTGCATGAAAAATGACAGTATTGAGGGGATTTACGATACCCTGAAGGAGTGTGCTGTAATTAGCAAGTCGGCCGGTGGCA
Basic information
species | Physcomitrella patens |
transcript | PP1S64_38V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S64_38V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 4
gttcggctatctattccttttgtgcgtgc-gctctttgcactgaaccaagcctggtc---agtcgtgaatgcgagtactaattggttgttcgaatgt--tgcagCTAAGCAGCTGTTTCCTACTGTGCATGAAAAATGACAGTATTGAGGGGATTTACGATACCCTGAAGGAGTGTGCTGTAATTAGCAAGTCGGCCGGTGGCA
|| | || | || || | || ||| ||| |||| | | || | | || | || ||||| |||||||||||||||| | ||||||||| ||||||| |||||||| || || ||||| ||||||| |||||||| || ||||| || || || || |
-------------------------gtactgcacatttgaccagaaaaatcctagtcttggactctgaaattgcttgcttactcttttattctctgcaatgcagTTAAGCAGCTGTTTCCTTATCTGCATGAAAGATGACAGCATTGAGGGAATCTATGATACTTTGAAGGAATGTGCTGTCATAAGCAAATCTGCTGGAGGAA
upper sequence: PP1S64_38V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 4
gttcggctatctattccttttgtgcgtgcgctctttgcactgaaccaagcc-tggtcagtcgtgaatgcgagtactaattggttgttcga-atgttgcagCTAAGCAGCTGTTTCCTACTGTGCATGAAAAATGACAGTATTGAGGGGATTTACGATACCCTGAAGGAGTGTGCTGTAATTAGCAAGTCGGCCGGTGGCA
|| | | ||| | || | | | | || || | | || |||| | || || || || ||||| ||||||||||||| || | ||||||||| ||||||| |||||||| || || || ||||||||||||||||||||||| ||||| || || || || |
---------------------gtactgtcttgcttcctgccagacgatgtcattgtgggttgaaattgtt--tacttactgtttcttttctgtgatgcagTTAAGCAGCTGTTTTCTTATATGCATGAAAGATGACAGCATTGAGGGAATCTATGAAACCCTGAAGGAGTGTGCTGTAATAAGCAAATCAGCTGGAGGAA
upper sequence: PP1S64_38V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 4
gttcggctatctattccttttgtgcgtgcgctctttgcactgaaccaagcc-tggtcagtcgtgaatgcgagtactaattg--gttgttcgaatgttgcagCTAAGCAGCTGTTTCCTACTGTGCATGAAAAATGACAGTATTGAGGGGATTTACGATACCCTGAAGGAGTGTGCTGTAATTAGCAAGTCGGCCGGTGGCA
|| | | || | | | | | | | || || |||| | || | | || | | || || ||||| ||||||||||||| || | ||||||||| ||||||| |||||||| || || || |||||||| |||||||||||||| ||||| || || || || |
---------------------gtactgtcttgtttcccgccagatgatgtcattgtgggttctgaaattgtttatttactgctgctttttctgtgatgcagTTAAGCAGCTGTTTTCTTATATGCATGAAAGATGACAGCATTGAGGGAATCTATGAAACCCTGAAAGAGTGTGCTGTAATAAGCAAATCTGCTGGAGGAA
upper sequence: PP1S64_38V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 4
-----------------------gttcggctatctattccttttgtgcgtgcgctctttgcactgaaccaagc-ctggtcagtcgtgaatgcgagtactaatt-----ggttgttcgaatg---ttgcagCTAAGCAGCTGTTTCCTACTGTGCATGAAAAATGACAGTATTGAGGGGATTTACGATACCCTGAAGGAGTGTGCTGTAATTAGCAAGTCGGCCGGTGGCA
|| | | | |||||| || | | ||| || | || | || | | | || | | || ||| | ||||| ||| |||||||| || || || ||||| ||||||||||| |||| ||||| |||||||| || || || |||||||||||||| | || ||||| || || || || |
gtatgtctgcattttattattcccttttgaaagtattatgttttgtctgt-cttttcttgtttgtaataatgcattagtgatttgatgatctgggctcttatttaagcgagtgttcatatgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGGATATATGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
upper sequence: PP1S64_38V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 4
-----------------------gttcggctatctattccttttgtgcgtgcgctctttgcactgaacca--agc---ctggtcagtcgtgaatgcgagtactaatt----ggttgttcgaatg---ttgcagCTAAGCAGCTGTTTCCTACTGTGCATGAAAAATGACAGTATTGAGGGGATTTACGATACCCTGAAGGAGTGTGCTGTAATTAGCAAGTCGGCCGGTGGCA
|| | || | |||| || || | |||| | | | || ||| || ||| | ||| | || || || | ||||| || |||||||| || || || ||||| |||| |||||| |||| ||||| |||||||| ||||| || |||||||||||||| | || ||||| || || || || |
gtatgattacattttaccatacccttttgaaattattatgttttctgtgttttatttttgtaataatgcattagcgaattgatcattgatgatctggggtcttatttaagcgagtgttcatgtgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGTATGAAAGATGATAGTATAGAGGGGATATACGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
upper sequence: PP1S64_38V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ14283 (Selaginella moellendorffii), 3'ss of exon 4
gttcggctatctattccttttgtgcgtgcgctctttgcactgaaccaagcctggtcagtcgtgaatgcgagtactaattggttgttcgaatgttgcagCTAAGCAGCTGTTTCCTACTGTGCATGAAAAATGACAGTATTGAGGGGATTTACGATACCCTGAAGGAGTGTGCTGTAATTAGCAAGTCGGCCGGTGGCA
||| || | | | | | || | | | |||| || || | | ||||| || ||||| ||||| || |||||||| | || || ||||| || ||||| |||||||||||||||||||| ||||| |||||||| ||||| || |
---------------------------------gttg-gttgcttcgtgattctccttttgtagttt--acttctaactg------tgacttctacagCTTAGTAGCTGCTTCCTTCTCTGCATGAAGGAGGATAGCATTGAAGGCATTTATGATACCCTGAAGGAGTGTGCAGTAATCAGCAAGTCAGCCGGGGGTA
upper sequence: PP1S64_38V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ20157 (Selaginella moellendorffii), 3'ss of exon 4
gttcggctatctattccttttgtgcgtgcgctctttgcactgaaccaagcctggtcagtcgtgaatgcgagtactaattggttgttcgaatgttgcagCTAAGCAGCTGTTTCCTACTGTGCATGAAAAATGACAGTATTGAGGGGATTTACGATACCCTGAAGGAGTGTGCTGTAATTAGCAAGTCGGCCGGTGGCA
|| || | || | || | ||| || || | || | | ||||| || ||||| ||||| || |||||||| | || || ||||| || ||||| |||||||||||||||||||| ||||| |||||||| ||||| || |
--------------------------------------gttggtt---gcttcgtgattctccttttgtagt-ttacttctcactgtgacttctacagCTTAGTAGCTGCTTCCTCCTCTGCATGAAGGAGGATAGCATTGAAGGCATTTATGATACCCTGAAGGAGTGTGCAGTAATCAGCAAGTCAGCCGGGGGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accaagcctggtcagtcgtgaatgcgagtactaattggttgttcgaatgttgcagCTAAGCAGCTGTTTCCTACTGTGCATGAAAAATGACAGTATTGAGGGGATTTACGATACCCTGAAGGAGTGTGCTGTAATTAGCAAGTCGGCCGGTGGCA
tactaat putative branch site (score: 1)
tactaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcggctatctattccttttgtgcgtgcgctctttgcactgaaccaagcctggtcagtcgtgaatgcgagtactaattggttgttcgaatgttgcagCTAAGCAGCTGTTTCCTACTGTGCATGAAAAATGACAGTATTGAGGGGATTTACGATACCCTGAAGGAGTGTGCTGTAATTAGCAAGTCGGCCGGTGGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG