Sequence
atgc intronic sequence ATGC exonic sequence...atatatatatatatatatatatatatatatcatcttatcatgtgtgtgtttgtgtttgttccgcattactgaacatcaccatcgactccgctgtttgcagTTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG
Basic information
| species | Physcomitrella patens |
| transcript | PP1S298_65V6.1 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S298_65V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g08880.2 (Oryza sativa), 3'ss of exon 2
atatatatatatatatatatatatatatatcatcttatcatgtgtgtgtttgtgtttgttccgcattactgaacatcaccatcgactcc---gctgtttg-cagTTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG
|| | | ||| ||| ||| | || | ||| | | | | ||| | | | |||| | | | || ||| | |||||||| |||||||| ||||||||||||||| | ||| | |||||||| ||| || ||
--atgctt-tgctggcctatgc-tatctattaaattgatttatgtattgcattaatatcatcattttatttgattttctcatccctttactaacaatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG
upper sequence: PP1S298_65V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g08880.3 (Oryza sativa), 3'ss of exon 2
atatatatatatatatatatatatatatatcatcttatcatgtgtgtgtttgtgtttgttccgcattactgaacatcaccatcgactcc---gctgtttg-cagTTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG
|| | | ||| ||| ||| | || | ||| | | | | ||| | | | |||| | | | || ||| | |||||||| |||||||| ||||||||||||||| | ||| | ||||
--atgctt-tgctggcctatgc-tatctattaaattgatttatgtattgcattaatatcatcattttatttgattttctcatccctttactaacaatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAAT-------------------
upper sequence: PP1S298_65V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G097726_T02 (Zea mays), 3'ss of exon 2
--atatatatatatatatatatatatatatatcatcttatcatgtgt--gtgtttgtgtttgttccgcattactgaacatcaccatcgactccgctgtttgcagTTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG
| || | | | | || | ||||| ||| | | || | ||| | ||||| || | | | | | | | ||| | |||||||||||||||||| |||||||| |||||| | ||| | ||||| || || |||||
atagatggaactttttttacttgtatatgtatttcttaaatctgaatcatcatttttacttgttttattcctctaatctcttctgtaaaacatg----tgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG
upper sequence: PP1S298_65V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA04G01140.1 (Glycine max), 3'ss of exon 2
atatatatatatatatatatatatatatatcatctt-atcatgtgtgtgtttgtgtttgttccgcattactgaacatca-ccatcgactccgctgtttgcagTTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG
| | || || | | | || ||| | |||| | || | | ||| | || | | | | | | |||||| ||||| || || |||||||||||||| ||||||||| | ||||| |||||||| ||||| |||||
--aaaatggtaagtagtagcttttttttagaatcgagaagctgtgggatcttatctagattctgacttgtgtgatgtaagttgtttaaaattttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG
upper sequence: PP1S298_65V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA12G35680.2 (Glycine max), 3'ss of exon 2
atatatatatatatatatatatatat-atatcatcttatcatgtgtgtgtttgtgtttgttccgcattactgaacatcaccatcgactccgctgtttgcagTTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG
|| | ||| | | | | | | | | || || || | | |||| || || ||| | || ||| | ||| | | ||||| || ||||||||||||||||||||||| || || |||||| | ||||| || ||||| ||||| || ||
gtaagtttatttctgttttttttagtgagataatgttgtaa-gtgtttgaaatggtgggttttgttttgttga---tttggttcggttttgtggtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
upper sequence: PP1S298_65V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA06G01180.2 (Glycine max), 3'ss of exon 1
atatatatatatatatatatatatatatatcatctt-atcatgtgtgtgtttgtgtttgttccgcattactgaacatca-ccatcgactccgctgtttgcagTTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG
| | || || | | || ||| | | || | || ||| ||| | | | | | | | | |||||| ||||| || || |||||||||||||| ||||||||| | ||||| ||||| || ||||| |||||
--aaaatggtaagtagcagctttttgttagaatcgagaagctttgggatcttatgtagattctgactcgtgtgatgtaagttgtttaaaattttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTG
upper sequence: PP1S298_65V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA13G34740.1 (Glycine max), 3'ss of exon 2
--atatatatatatatatatatatatatatatcatcttatcatgtgtgtgttt-gtgtttg-----ttccgcattact--gaacatcaccatcgactccgctgtttgcagTTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG
| | | | ||| | | | | || | || || | | | ||||| || ||||||| | | || | | || | | | | |||| || ||||||||||||||||||||||| || || |||||| | ||||| || ||||| ||||| || ||
gtaagtttttttatttctgtttttactgagataatggtgttgtttgtgttttaagtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
upper sequence: PP1S298_65V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA13G34740.3 (Glycine max), 3'ss of exon 2
--atatatatatatatatatatatatatatatcatcttatcatgtgtgtgttt-gtgttt-----gttccgcattact--gaacatcaccatcgactccgctgtttgcagTTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG-------------------------------
| | | | ||| | | | | || | || || | | | ||||| || |||||| | | | || | | || | | | | |||| || ||||||||||||||||||||||| || || |||||| | ||||| || ||||| ||||| || ||
gtaagtttttttatttctgtttttactgagataatggtgttgtttgtgttttaagtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGGTAAAACCAGTATATTCTGCTTTTTTTTGTT
upper sequence: PP1S298_65V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT4G39100.1 (Arabidopsis thaliana), 3'ss of exon 2
atatatatatatatatatatat-atatatatca-tcttatcatgtgtgtgtttgtgtttgttccgcattactgaacatcaccatcgactccgctgtttgcagTTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG
| ||| || || || | | || || || | | || | || ||| |||| || | | | | | | | |||||||||| | |||||||| |||||||| || || || |||||||||||||| ||||| || || || ||
gttaata-attcattgatttgtcatctaaattggtttcatgaagt-tgtttttgcaaagagaagtaatcaattgagtttaaattgattttttctgtttgcagGTTCTGCAAGTGTGAGATGCCGTATAACCCAGATGACTTGATGGTGCAATGCGAGGAGTGTTCTGAGTG
upper sequence: PP1S298_65V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ17782 (Selaginella moellendorffii), 3'ss of exon 2
----------------------------------------------------------------------------atatatatatatatatatatatatatatatcatcttatcatgtgtgtgtttgtgtttgttccgcattactgaacatc--accatcgactccgctgtttgcagTTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG
| | | | | | | ||| | | || | | | |||||| | || | | | || || |||| || | || || ||||||||||| |||||||| |||||||| || || ||||||||||| || || |||||| || ||
gtaagtgctctctctctccctctgtctctctggcgtctcgttgactagttgtgttcttatcaagcttctctttcttctcttggtctcgttgtgttcttatcgaacttctcctgttctcgttgtgttcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAGTGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtttgtgtttgttccgcattactgaacatcaccatcgactccgctgtttgcagTTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG
ctccgct CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatatatatatatatatatatatatatatcatcttatcatgtgtgtgtttgtgtttgttccgcattactgaacatcaccatcgactccgctgtttgcagTTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaaca
