Sequence
atgc intronic sequence ATGC exonic sequence...ggcgcagagagctaaattttagcctggcgaaggtcgaagttgttgagggtcatatcctggtctgaggatgttggggggtgtattgtgtgttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
Basic information
| species | Physcomitrella patens |
| transcript | PP1S131_139V6.1 |
| intron # | 1 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os04g55970.2 (Oryza sativa), 3'ss of exon 2
ggcgcagagagctaaattttagcctggcgaaggtcgaagttgttgagggtcatatcctggtctgaggat---gttggggggtgtattgtg--tgttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
|| |||| | | || |||| | | || || || ||| | || ||| | | | || | || | ||||||||| ||||| ||| |||||||||| ||||||||||| || | || | || || || | ||||| || || ||||
-----tagtagtagttttttttgttaatgggagtagaagaatcaaatgaccaatatttgttcagagattttaattagggcataaaaaatccttggttatgtatagGCATCGGTGGACCGGAAGGTACGAGGCGCATCTGTGGGATAACAGCTGCCGGCGTGAGGGCCAGAGCCGCAAGGGACGCCAAG
upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g07940.1 (Oryza sativa), 3'ss of exon 2
ggcgcagagagctaaattttagcctggcgaaggtcgaagttgttgagggtcatatcctggtctgaggatgttggggggtgtattgtgtgttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
| | | | ||| || | | | | || | | ||| | ||| || |||| | | || | | ||| || ||| | ||||||||| | ||||||||||| |||||||||| ||||| || |||||||| || || | ||||| | ||||
---gttggtgacgacattgctgcttctccattgc-----ttccggcgtgtctca--ctgatcc----atgtctacgtgctcatcattt-----ttttcagACATAGATGGACTGGAAGATACGAGGCTCACTTGTGGGACAACACTTGCAGGAAGGAAGGCCAGACCAGGAAAGGAAGGCAAG
upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G399072_T02 (Zea mays), 3'ss of exon 2
----------------------ggcgcag-agagc-taaattttagcctggcgaaggtc----gaagttgttgagggtcatatcc-tggtctgaggatgttggggggtgtattgtgtgttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
||||| || || | || | || | | || | || ||| | ||| | ||| || | | || || || | || || ||||| | ||||| || |||||||||||||| ||||||||||| ||||| || |||||||| || ||| | ||||| | ||||
gttggccttagttgatgtgctgcgcgcatcagcgcatgcatgcgtacatgctcaggatctcgcaacgtcgttcctagcttgatcgatcgtcctgatgcgtgcgtgtgtctaa-atggatctatctgcagGCACAGATGGACCGGGCGGTACGAGGCTCACCTGTGGGACAACACTTGCAGGAAGGAAGGCCAGACTAGGAAAGGGAGGCAAG
upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G399072_T03 (Zea mays), 3'ss of exon 2
----------------------ggcgcag-agagc-taaattttagcctggcgaaggtc----gaagttgttgagggtcatatcc-tggtctgaggatgttggggggtgtattgtgtgttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG-----------------
||||| || || | || | || | | || | || ||| | ||| | ||| || | | || || || | || || ||||| | ||||| || |||||||||||||| ||||||||||| ||||| || |||||||| || ||| | ||||| | ||||
gttggccttagttgatgtgctgcgcgcatcagcgcatgcatgcgtacatgctcaggatctcgcaacgtcgttcctagcttgatcgatcgtcctgatgcgtgcgtgtgtctaa-atggatctatctgcagGCACAGATGGACCGGGCGGTACGAGGCTCACCTGTGGGACAACACTTGCAGGAAGGAAGGCCAGACTAGGAAAGGGAGGCAAGGTGAGTGAGAGCTTAGC
upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G086573_T01 (Zea mays), 3'ss of exon 2
-ggcgcagagagctaaattttagcctggcgaaggtcgaagttgttgagggtcatatcctggtctgaggatgttggggggtgtattgtgtgt--tgatttgtagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
| | | | | | | | ||| | | | | || |||| | || |||| | || || || | ||| | | | | |||||| |||||| || |||||||| |||||||||| |||||||||||||| | || || ||||| || | ||||| || || ||||
agaaaaaaataacaagcagtcaagctgcaccatatattattaattacgggttttgtct--gtctaaa-atcttaggtgatgtggtatttttggtgatttctagGCACCGGTGGACTGGCAGGTACGAGGCACATCTGTGGGACAACAGCTGCCGACGCGAAGGGCAGAGCCGCAAGGGCCGCCAAG
upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G366434_T01 (Zea mays), 3'ss of exon 2
ggcgcagagagctaaattttagcctggcgaaggtcgaagttgttgagggtcat-atcctggtctgaggatgttggggggtgtattgtgtgttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
| | | || || | | || || | | | | | | | | | | | || || | | | | || | | ||| |||||| | ||||| || ||||| ||||||||||| ||||| |||| |||||||| |||||| || | |||||| ||| | ||||
tatatatatatatatatatatacgtgttgaggttggtaataacaaatgtttttgaaaacgcactatatatat-gcataattttgagtattcttgtttacagGCATAGATGGACAGGGCGGTATGAGGCTCATCTATGGGATAATAGTTGTAGAAGGGAAGGGCAGAGTCGCAAGGGTAGGCAAG
upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA17G07010.1 (Glycine max), 3'ss of exon 2
ggcgcagagagctaaattttagcctggcgaaggtcgaagttgttgagggtcatatcctggtctgag----gatgttggggggtgtattgtgtgt-tgatttgtagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
|| | | | | | || | ||||| | | | || || || ||| ||| | | |||| || ||| | |||||||| | ||||| |||||||| |||||||||| ||| |||| ||||||||||| | ||||| | ||||
------------------gtatcttattcatgaccaccaccttttatcatcataatataatattagtaattattttatttatctgattctgtttcttattttcagACATAGATGGACTGGGAGATACGAAGCTCATCTATGGGACAATAGTTGCAGAAGGGAAGGTCAAAGCAGGAAAGGAAGGCAAG
upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA18G47980.1 (Glycine max), 3'ss of exon 5
----ggcgcagagagctaaattttagcctggcgaaggtcgaagttgttgagggtcatatcctggtctgaggatgttggggggtgtattgtgtgttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
| | | ||||| | | | || | || || ||| |||| || || ||| | | ||| |||||| | ||||| || |||| |||||||| |||||||| |||| |||||||| || || |||||||||||||| | ||||
agtctgttttcattgtcgtatttttaaaaaa-aatatttattgcatttttaaaaaaaattgtgaaatgatgatgaaattaggggttttg---acttaattgaagGCATAGGTGGACGGGGAGGTATGAGGCTCACCTGTGGGATAATAGTTGTAGAAGAGAGGGACAAACTCGCAAAGGAAGGCAAG
upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA16G00950.1 (Glycine max), 3'ss of exon 4
----ggcgcag-agagctaaattttagcctg---gcgaaggtcg--aagttgttgagggtcatatcctggtctgaggatgttggggggtgtattgtgtgttga-----------tttgt-agGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
|| | | || | ||| ||| | || || | | ||| || | | | | | ||| | | || | | ||| ||||| |||||| | ||||||||| | || ||||| ||| ||||||| |||| ||| ||||||||||| ||||| | ||||| | ||||
gttaggagtaatggattttaatgttaatttttttaaaaaaatcatcacatagtttagtactttgtttattttgatgaactttgcttctttttttttcttttggggttcatggattttgttagGCATAGATGGACTGGAAGATATGAGGCCCATTTGTGGGATAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG
upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA07G04260.1 (Glycine max), 3'ss of exon 3
---ggcgcag-agagctaaattttagcctggcgaaggtcgaagttgttgagggtcatatcctggtctgaggatgttggggggtgtatt-------gtgtgttgatttg--tagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
|| | | ||| | ||| || | | || | | | ||| || | | | | | || ||| | | | || | ||||| ||||||| | |||||||| | || ||||| ||| |||||||||||| ||| ||||||||||| ||||| | ||||| | ||||
gtaggagtaatagattttaatgttttttt--taattgttgca-tggtttagtgctttgtttattttgatgaattttgctcttttttcttttcgtggttcctggattttgttagGCATAGATGGACTGGGAGATATGAGGCCCATTTGTGGGACAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG
upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT3G20840.1 (Arabidopsis thaliana), 3'ss of exon 2
ggcgcagagagctaaattttagcctggcgaaggtcgaagttg--ttgagggtcatatcctggtctgaggatgttggggggtgtattgtgtgttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
| || || | | || | | | ||| | | || | || ||| || | | | || ||| | | ||| ||||| |||||||| || || ||||||||||| ||||| |||| |||||||| |||||| || || | ||||| ||||||
----------gttagatatgtgactcatcactcttttacttgattctttaatgattttgtgatcttt--atttgagtgtaatgatgaaatgtgcacatatagACATCGATGGACTGGTCGATATGAGGCTCATCTATGGGATAATAGTTGTAGAAGGGAAGGCCAGTCTAGGAAAGGAAGACAAG
upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ21317 (Selaginella moellendorffii), 3'ss of exon 2
ggcgcagagagctaaattttagcctggcgaaggtcga-agttgttgagggtcatatcctggtctgaggatgttggggggtgtattgtgtgttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
| | |||| | | |||| | |||| || | || | | | || | | |||||||| ||||||||||| |||||||| |||||||||||||||| |||| ||||||| || || || | ||||| | ||||
-------------------------gtacgtgatcgacaacttttgatcgatatatggagg---aaccatagctagactaatcacgggtttgatggagCAGGCATCGCTGGACTGGACGTTACGAGGCACATCTGTGGGACAATAGTTGTCGAAAGGAGGGCCAGACCAGGAAAGGGAGGCAAG
upper sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 2
ggcgcagagagctaaattttagcctggcgaaggtcga-agttgttgagggtcatatcctggtctgaggatgttggggggtgtattgtgtgttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
| | |||| | | |||| | |||| || | || | | | || | | |||||||| ||||||||||| |||||||| |||||||||||||||| |||| ||||||| || || || | ||||| | ||||
-------------------------gtacgtgatcgacaacttttgatcgatatatagagg---aaccatagctagtctaatcacgggtttgatggagCAGGCATCGCTGGACTGGACGTTACGAGGCACATCTGTGGGACAATAGTTGTCGAAAGGAGGGCCAGACCAGGAAAGGGAGGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agggtcatatcctggtctgaggatgttggggggtgtattgtgtgttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
tgttgat putative branch site (score: 4)
ttgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggcgcagagagctaaattttagcctggcgaaggtcgaagttgttgagggtcatatcctggtctgaggatgttggggggtgtattgtgtgttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
