Sequence
atgc intronic sequence ATGC exonic sequencegtacgtgatcgcacgtgtgttcattgtaaagcttcaacagattgatttgtgtggtatcgttttgcatgatgcattcttccattatcaatgtcgatagaatcctaatgtatccacttattgtcctgcagACATACATTCGACCAGAAGCGTCTGAAGCAGCCTCTGTACCGGCACCCATGGGAGGATGTGTTGTACACCAAGTACACATAA
Basic information
species | Physcomitrella patens |
transcript | PP1S46_63V6.3 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S46_63V6.3 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GRMZM2G045534_T01 (Zea mays), 3'ss of exon 4
----------------------------gtacgtgatcgcacgtgtgttcattgtaaagcttcaac---agattg-atttgtgtggtatcgttttgcatgatgcattcttccattatcaatgtcgatagaatcctaatgtatccacttattgtcctgcagACATACATTCGACCAGAAGCGTCTGAAGCAGCCTCTGTACCGGCACCCATGGGAGGATGTGTTGTACACCAAGT-ACACATAA-----------------
| || | | || | || ||||||| | || | ||| | || | | | || | || ||| || || | ||| | | ||| | | |||| ||| || || |||||||||||| | || |||||||| || ||||| ||||||||||||||||| |||||||||||| | | | |
gtgagtcctattctgctgttaattgaatcttcgggtttgc-tacgcattgattgtaatgtttgggtcttatgttgcagttatatattttcatgttt--tgaccatttgttatacgtacaagacaagccgttttttaaaatgtgt-tacattgattcacagGCACACCTTCGACCAGAAGAGGCTTAAGCAGCCACTCTACCGCCACCCATGGGAGGATGTCCTGTACACCAAGTGAGATAGAGCCATTCTTTGCAAAGCA
upper sequence: PP1S46_63V6.3 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GRMZM2G002416_T01 (Zea mays), 3'ss of exon 11
----gtacgtgatcgcacgtgtgttcattgtaaagcttcaacagattgatt------tgtgtggtatcgttttgca-tgatgcattcttcc--att-----------atcaatgtcgatagaatcct----aatgtatccact-tattgtcctgcagACATACATTCGACCAGAAGCGTCTGAAGCAGCCTCTGTACCGGCACCCATGGGAGGATGTGTTGTACACCAAGTACACATAA------------------
|| | || | | || ||| | | || | | ||||| | || ||| | | ||||| | || ||| | || ||| || | | | | | | || || | ||| ||| ||||| |||||||||||| | || |||||||| || ||||| ||||||||||||||||| | |||||||||| |
gtgagtccttgctgttaattgaattctctttggctctgctttgcaatgattgtaatgtttggggtcttatgttgcagtaatatattttcccctattttggccatttgatttacagcaagcaacttttctgaaaaaaatgtgttactttgattcacagGCATACCTTCGACCAGAAGAGGCTCAAGCAGCCACTCTACCGTCACCCATGGGAGGATGTACTTTACACCAAGTGAGAAAGCCATTCTTTGCAAGGCATA
upper sequence: PP1S46_63V6.3 (Physcomitrella patens), 3'ss of exon 14
lower sequence: AT3G06650.1 (Arabidopsis thaliana), 3'ss of exon 16
gtacgtgatcgcacgtgtgttcattgtaaagcttcaacagattgatttgtgtggtatcgttttgcatgatgcattcttccattatcaatgtcgatagaatcctaatgtatccacttattgtcctgcagACATACATTCGACCAGAAGCGTCTGAAGCAGCCTCTGTACCGGCACCCATGGGAGGATGTGTTGTACACCAAGTACACATAA------------------
| ||| || | | | | | | | | | ||| | || || | | | | | | | ||||| || |||||||| |||||| | ||||||||||| |||||||| ||||| ||||| ||||| |||||||||||||| ||||
--------------------------------------------gtaactgtcataaccaaacactt-acacttgttcttaaaacaaatttaaattgatgtggattacgtgaataaaat-tgttgcagGCACACATTCGATCAGAAGAGACTGAAGCAGCCACTGTACCGACACCCGTGGGAAGATGTCTTGTACACCAAGTAATCATATCATTATTCACTTCTTCTG
upper sequence: PP1S46_63V6.3 (Physcomitrella patens), 3'ss of exon 14
lower sequence: Vv05s0077g00950.t01 (Vitis vinifera), 3'ss of exon 16
---------------gtacgtgatcgcacgtgtgttcattgtaaagcttcaacagattgatttgtg--tggtatcgttttgcatga-tgcat--tcttccattatcaatgtcgatagaatcctaat--gtatccacttatt---gtcctgcagACATACATTCGACCAGAAGCGTCTGAAGCAGCCTCTGTACCGGCACCCATGGGAGGATGTGTTGTACACCAAGT---ACACATAA---------------
| | || | | | | | | || | | | | | | ||| || | ||||| | ||||| | || | | || || || || |||| | | ||| || || |||||||||||| | |||||||||| || ||||| ||||||||||||||||| | |||||||||| | || ||
gtaagttggcttacacttcagagtccctttcctttctacctttctggtttattctctccctccatttctaccttaaacttggatcactgcatcatattccacttcaaacgcatagtttcctctgattggtttcttcttaattcaaaacctcagGCACACTTTCGACCAGAAGAGATTGAAGCAGCCCCTATACCGTCACCCATGGGAGGATGTCCTCTACACCAAGTGAGAAACTTACAGATTGCCGACACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttccattatcaatgtcgatagaatcctaatgtatccacttattgtcctgcagACATACATTCGACCAGAAGCGTCTGAAGCAGCCTCTGTACCGGCACCCATGGGAGGATGTGTTGTACACCAAGTACACATAA
tcctaat putative branch site (score: 2)
ttgtcct putative PPT
attatcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtgatcgcacgtgtgttcattgtaaagcttcaacagattgatttgtgtggtatcgttttgcatgatgcattcttccattatcaatgtcgatagaatcctaatgtatccacttattgtcctgcagACATACATTCGACCAGAAGCGTCTGAAGCAGCCTCTGTACCGGCACCCATGGGAGGATGTGTTGTACACCAAGTACACATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG