Sequence
atgc intronic sequence ATGC exonic sequencegtgaatgctattgctggcccctctctcacaaccatcatcttgctattctttttaaacagtcaatgtgatgatatcgttcattagctcttagtatgctcctactgttatgtacggttcttatccaaacagatccatgagaaacacagttctcacttccgactgcagATTATCAGTCAATTGTGGAAGGAAATTATGAAGAGATGTCCACAACTGAACTTTCTGGAGGAGCACGTATACACTACATTTTCCAAGAAATTTTTGTCAG
Basic information
species | Physcomitrella patens |
transcript | PP1S82_15V6.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S82_15V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G180335_T01 (Zea mays), 3'ss of exon 8
gtgaatgctattgctggcccctctctcacaaccatcatct-tgctattctttttaaacagtcaatgtgatgatatcgttcattagctcttagtatg--ctcctactgttatgtacggttcttatccaaacagatccatgagaaacacagttctcacttccgactgcagATTATCAGTCAATTGTGGAAGGAAATTATGAAGAGATGTCCACAACTGAACTTTCTGGAGGAGCACGTATACACTACATTTTCCAAGAAATTTTTGTCAG
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---------------------------gtaaatatgaaccatgtcactttttctaaggaaactatgtg------tgccccaataatagttagaattgcctattactttcatgt---gtctttat--------atttttaaacattaaataacctatgtat-actgtagCTTTTTCGTCAATGGTGGAAGGAAAAAATGAAGATATATCGACAACTGAACTTTCTGGTGGAGCGAGGATCCATTACATTTTCCAGTCTATCTTTGTCAA
upper sequence: PP1S82_15V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G129155_T02 (Zea mays), 3'ss of exon 8
gtgaatgctattgctggcccctctctcacaaccatcatcttgctattctttttaaacagtcaatgtgatgatatcgttcattagctcttagtatgctcctactgttatgtacggttcttatccaaacagatccatgagaaacacagttctcacttccgactgcagATTATCAGTCAATTGTGGAAGGAAATTATGAAGAGATGTCCACAACTGAACTTTCTGGAGGAGCACGTATACACTACATTTTCCAAGAAATTTTTGTCAG
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---------------------------gtaaatattgaactatgacacttttgttaaggaaactatatttatgccctataattgctagaattgc-ctattactttcctgtgttgtgcttttatattttgagcattaaataacctgtgtat--------actgtagCTTTCTCCTCAATGGTGGAAGGAAAAAATGAAGATATATCGACAATTGAACTCTCTGGTGGAGCAAGGATCCATTACATTTTCCAGTCTATCTTTGTCAA
upper sequence: PP1S82_15V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EFJ15047 (Selaginella moellendorffii), 3'ss of exon 8
gtgaatgctattgctggcccctctctcacaaccatcatcttgctattctttttaaacagtcaatgtgatgatatcgttcattagctcttagtatgctcctactgttatgtacggttcttatccaaacagatccatgagaaacacagttctcacttccg-actgcagATTATCAGTCAATTGTGGAAGGAAATTATGAAGAGATGTCCACAACTGAACTTTCTGGAGGAGCACGTATACACTACATTTTCCAAGAAATTTTTGTCAG
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------------------------------------------------------------------------------------------------------------gtacg----ttagactgaaaaagtaatctgcattttaattctttttcctgcatttcagGTTTTTCATCAGTTGTGGATGGCAAAAACGAAGAGATGTCAACTGTTGAACTATCTGGAGGAGCTCGTATTCACTACATATTCCAATCAATTTTCGTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acggttcttatccaaacagatccatgagaaacacagttctcacttccgactgcagATTATCAGTCAATTGTGGAAGGAAATTATGAAGAGATGTCCACAACTGAACTTTCTGGAGGAGCACGTATACACTACATTTTCCAAGAAATTTTTGTCAG
ttctcac putative branch site (score: 2)
ttctcacttcc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaatgctattgctggcccctctctcacaaccatcatcttgctattctttttaaacagtcaatgtgatgatatcgttcattagctcttagtatgctcctactgttatgtacggttcttatccaaacagatccatgagaaacacagttctcacttccgactgcagATTATCAGTCAATTGTGGAAGGAAATTATGAAGAGATGTCCACAACTGAACTTTCTGGAGGAGCACGTATACACTACATTTTCCAAGAAATTTTTGTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA