Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaactgaagcctaacacctgtttcgacctctatatctgcagATGGCCGACCCTTTGACTGCTCTTATGCACGCAGTTCAAGTGATGAACTTGCTGAAGACGTTGATACTACGAACCTTGAAAGACAGAGAGGAGGCGATAT
Basic information
species | Physcomitrella patens |
transcript | PP1S13_243V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S13_243V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os02g45600.1 (Oryza sativa), 3'ss of exon 4
gtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaactga-agcctaa-cacctgtttcgacctctatatctgcagATGGCCGACCCTTTGACTGCTCTTATGCACGCAGTTCAAGTGATGAACTTGCTGAAGACGTTGATACTACGAACCTTGAAAGACAGAGAGGAGGCGATAT
| || || | |||| || ||| || |||| || |||| | | || |||| || | | ||| | | | |||||||||| || ||||||||| | || || ||||||||||||||||| || || ||||| | || | || |||| | | || || |
------------------------------gttattctcaaaatctatttggctttatttattttttcttgctatctacagaatttgctatttcacagactaatcatgtaacataccatctct-tttatagATGGCCGATCCCTTGACTGCTTTGATACATGCAGTTCAAGTGATGAATTTTCTCAAGACACTTATCTTGAAGACTGTGAAGGGACGGGAAGAAACAGCTA
upper sequence: PP1S13_243V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA12G09560.1 (Glycine max), 3'ss of exon 5
gtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaactgaagcctaacacctgtttcgacctctatatctgcagATGGCCGACCCTTTGACTGCTCTTATGCACGCAGTTCAAGTGATGAACTTGCTGAAGACGTTGATACTACGAACCTTGAAAGACAGAGAGGAG-GCGATAT
| ||| || | || | | | || || ||| | ||| || || | || || || | || | || || || | | |||||||||| |||||||||||||| | ||| | |||||||||||||||||||| ||||||| | ||| || | ||| || ||| ||| || | | |
--gtgccatttttg-----tccatagagtagtga-----agatgccaat-gtgat---------acagttgatct-atctta------tggttggtttcagttacagaatttagtctttttggttgcagATGGCAGACCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTGAAGAATCTTATATTAAGGACCCTGCGAGAAAGAAAGTATTGTGTCG-
upper sequence: PP1S13_243V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA03G42090.1 (Glycine max), 3'ss of exon 4
gtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaactgaagcctaacacctgtttcgacctctatatctgcagATGGCCGACCCTTTGACTGCTCTTATGCACGCAGTTCAAGTGATGAACTTGCTGAAGACGTTGATACTACGAACCTTGAAAGACAGAGAGGAGGCGATAT
|| | || || | || || | || ||| | | ||| | || | || | | | | | || |||||| | | |||||||||| |||||||||||||| | || || ||||| |||||||||||||| || ||||| ||||| || ||| | ||| ||||| | | ||
-----------------------tttcttcctaccagt-gaggcccgtataactgtttgtatgcacatgttactt-atgctagtg-gatgtggatatttaaatgtttgtttcattgtgc---tttgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTGATGAACTTTCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATAAATCAATTG
upper sequence: PP1S13_243V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA11G18900.1 (Glycine max), 3'ss of exon 6
gtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaactgaagcctaacacctgtttcgacctctatatctgcagATGGCCGACCCTTTGACTGCTCTTATGCACGCAGTTCAAGTGATGAACTTGCTGAAGACGTTGATACTACGAACCTTGAAAGACAGAGAGGAGGCGATAT
| ||| || | || | | | || || ||| | ||| | || | | || || | | | | | || || || | | |||||||||| || ||||||||||| | ||| | |||||||||||||||||||| || |||| | ||| || | || || ||| ||| |||| |
--gtgccatttttg-----tccatagagtagtga-----agatgccaat-gtgatatagttga-----tctatcttatggtaggtttc-agttacag----------aatttagtctttctggttgcagATGGCAGATCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTAAAGAATCTTATATTAAGGACACTGCGAGAGAGAAAGGATTGTGTGG
upper sequence: PP1S13_243V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA19G44820.1 (Glycine max), 3'ss of exon 4
gtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactctt-cacctcattttggaacgctaactgaagcctaacacctgtttcgacctctata-tctgcagATGGCCGACCCTTTGACTGCTCTTATGCACGCAGTTCAAGTGATGAACTTGCTGAAGACGTTGATACTACGAACCTTGAAAGACAGAGAGGAGGCGATAT
||| || | || | | || | | | | || || || | |||| | |||| || ||| || || | |||| | |||||||||| |||||||||||||| | || || ||||| ||||| |||||||| || ||||| ||||| || ||| | ||| ||||| || | ||
-----------------------ttgtat-cacatttttaactttttcttcctaccagtgaggcccttttacatgttattt----atgctagtggatatttaaa---tggttgcttcactatgctatgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTCATGAACTTCCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATGAATCAATTG
upper sequence: PP1S13_243V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaactgaagcctaacacctg--tttcgacctctatatctgcagATGGCCGACCCTTTGACTGCTCTTATGCACGCAGTTCAAGTGATGAACTTGCTGAAGACGTTGAT-ACTACGAACCTTGAAAGACAGAGAGGAGGCGATAT
| | | || | | | | | | | | | || | | |||||| || | | | ||| || ||| ||||| | || || || || ||||||||||| || |||||||||||||||||||| ||||| | || || | || || | || | || | | ||
-----------------------------------------------gtaaaaacaaagttaacctttgttcaatgaataagaatcactgagtagttactaacatttgattcttgcattctctaactgtagATGACAGATCCATTAACGGCTCTTATGCATGCTGTTCAAGTGATGAACTTGCTTAAGACTCTTATCACAAAGACACTAGCTGAACGGGAAGAAAATGCTA-
upper sequence: PP1S13_243V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT2G46710.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaactgaagcctaacacctgtttcgacctctatat-ctgcagATGGCCGACCCTTTGACTGCTCTTATGCACGCAGTTCAAGTGATGAACTTGCTGAAGACGTTGATACTACGAACCTTGAAAGACAGAGAGGAGGC-GATAT
| || | |||| ||| | ||||| |||| | || | ||| | | || | | | | | | | | || || ||||||| || ||||| ||||| || || |||||||| |||||||||||||| || ||||| ||||| || | | | ||||| || || | || ||
--------------------------------gtcagt--aataaaattga--attttcttttaatgaaacagttgattctttagttatat---agttttgaatctcatgaaaatgttttgatgttgtagATGGCAGATCCTTTAACTGCACTCATCCACGCAGTGCAAGTGATGAACTTTCTCAAGACTTTGATCTTAATGAACCTCAAAGAAAGGGAAAACGCAGACG-
upper sequence: PP1S13_243V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaactgaagcctaacacctgtttcgacctctatatctgcagATGGCCGACCCTTTGACTGCTCTTATGCACGCAGTTCAAGTGATGAACTTGCTGAAGACGTTGATACTACGAACCTTGAAAGA-CAGAGAGGAGGCGATAT
| ||| | |||||| | || |||| | | ||| ||| | | || || ||| ||| ||| | | || || |||||| | || || ||||| ||||| ||||| || |||||||||||||||||||| ||||| |||| | ||| | | || | | || | ||
-----------------------gttgatattaaatcttgaaaatttcttg----ttttagctaatgctttggtccat----ggatttcaat--aaatagaactccttttttg--tttgatttcaccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcattttggaacgctaactgaagcctaacacctgtttcgacctctatatctgcagATGGCCGACCCTTTGACTGCTCTTATGCACGCAGTTCAAGTGATGAACTTGCTGAAGACGTTGATACTACGAACCTTGAAAGACAGAGAGGAGGCGATAT
gcctaac putative branch site (score: 2)
cctctat putative PPT
tctatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaactgaagcctaacacctgtttcgacctctatatctgcagATGGCCGACCCTTTGACTGCTCTTATGCACGCAGTTCAAGTGATGAACTTGCTGAAGACGTTGATACTACGAACCTTGAAAGACAGAGAGGAGGCGATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG