Sequence
atgc intronic sequence ATGC exonic sequence...ttgtgcaaaatcaacattccgaccaatctcttgtcgtgatatttctgaaaccgtagaaaaattaacaatgtgtcccaaccctgccttaattattttgaagGTCGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAAAGAGACGGATGGAGTCATGGTGGCCAGAGGTGACCTGGGTATGGAGATTCCAACAG
Basic information
species | Physcomitrella patens |
transcript | PP1S90_134V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S90_134V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA02G07800.1 (Glycine max), 3'ss of exon 3
ttgtgcaaaatcaacattccgaccaatctcttgtcgtgatatttctgaaaccgtagaaaaattaacaatgtgtcccaaccctgccttaattattttga--agGTCGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAAAGAGACGGATGGAGTCATGGTGGCCAGAGGTGACCTGGGTATGGAGATTCCAACAG
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-tgtataagttccctatacaagtctatgaaaataagaaacagttcttgtattgattaacctcccaaattgtacttatttgttgtcttc-ttgttttggttagGTTGAAAATCAAGAGGGTGTTGCCAATTTTGATGAAATACTGGCAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
upper sequence: PP1S90_134V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA16G26830.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------------------ttg--tgcaaaatcaacattccgaccaatctcttgtcgtgatatttctgaaaccgtagaaaaa---ttaacaatg-----tgtcccaaccctgccttaattat----tttga-agGTCGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAAAGAGACGGATGGAGTCATGGTGGCCAGAGGTGACCTGGGTATGGAGATTCCAACAG
||| | | |||| | || || |||| | | |||| | | ||| | || || | |||||| |||| || | |||| |||| || || || || ||| | | || || || || ||| || || | | |||| | |||||||||| |||||||||||||| ||||| ||||||| |
gtatccatccttattctcaagtaaatgtattctgttttactttaactcttcaaataatttacagaaatgtcattttactttcactttgattctattttcaaacatacgtataagctctccgtacaagtctatgaaaacaagaaacaaagttctggcattgattaatctcccaaattgtacttatttgttgtctttgttagGTTGAAAATCAAGAGGGTGTTGCAAATTTTGATGAAATACTGGAAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
upper sequence: PP1S90_134V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ36162 (Selaginella moellendorffii), 3'ss of exon 2
ttgtgcaaaatcaacattccgaccaatctcttgtcgtgatatttctgaaaccgtagaaaaattaacaatgtgtcccaaccctgccttaattattttgaagGTCGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAAAGAGACGGATGGAGTCATGGTGGCCAGAGGTGACCTGGGTATGGAGATTCCAACAG
|| | | || | | | || || | ||| || | | || || | | || |||||||||||||||| ||||| ||||||||||| || | ||| |||| | ||||||||||||| || || || || |||||||| ||||| |
------------------------------gtgggctttttctttcgtttctcttgatggatcatagttgt-tctta--cgtgatctattggaagtttagATCGAGAACCAGGAAGGACTGGTGAACTTCGACGAGATCCTCCGTGAGTCGGACGCGATCATGGTGGCCAGGGGCGATCTCGGCATGGAGATCCCAACGG
upper sequence: PP1S90_134V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ18654 (Selaginella moellendorffii), 3'ss of exon 2
ttgtgcaaaatcaacattccgaccaatctcttgtcgtgatatttctgaaaccgtagaaaaattaacaatgtgtccca-accctgccttaattattttgaagGTCGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAAAGAGACGGATGGAGTCATGGTGGCCAGAGGTGACCTGGGTATGGAGATTCCAACAG
| | || | | | | ||| | || | | | | | || | | | ||| ||| || |||||||||||||||| ||||| ||||||||||| || | ||| |||| | ||||||||||||| || || || || |||||||| ||||| |
---------------------gttagctttttctttcgtttctcttga-----tgga-----tcatagtttttcttacatgatctcttggaagttt---agATCGAGAACCAGGAAGGACTGGTGAACTTCGACGAGATCCTCCGTGAGTCGGACGCGATCATGGTGGCCAGGGGCGATCTCGGCATGGAGATCCCAACGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaaccgtagaaaaattaacaatgtgtcccaaccctgccttaattattttgaagGTCGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAAAGAGACGGATGGAGTCATGGTGGCCAGAGGTGACCTGGGTATGGAGATTCCAACAG
ttatttt CT-rich tract
tagaaaaattaacaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtgcaaaatcaacattccgaccaatctcttgtcgtgatatttctgaaaccgtagaaaaattaacaatgtgtcccaaccctgccttaattattttgaagGTCGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAAAGAGACGGATGGAGTCATGGTGGCCAGAGGTGACCTGGGTATGGAGATTCCAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT