Sequence
atgc intronic sequence ATGC exonic sequencegtatggaagaatttgtagcctctagactctagagcattccaacttctgcaagaatggtaaatctttgacaaaggttgggatcacagAGGATTGCGCGAGCTCGGCAGATCAGAGCGAGTGGTACTTCTTCAGCCACAAAGACAAGAAGTATCCGACCGGGAGCCGAACCAACAGGGCCACAACAGC
Basic information
species | Selaginella moellendorffii |
transcript | EFJ24736 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ08057 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S6_458V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------------------------------------------------------------gtatggaagaatttgta-gcctctagactctagagcattccaacttctgcaagaatggtaaatctttg-acaaaggttgggatcacagAGGATTG----CGCGAGCTCGGCAGATCAGAGCGAGTGGTACTTCTTCAGCCACAAAGACAAGAAGTATCCGACCGGGAGCCGAACCAACAGGGCCACAACAGC
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gtaagccaacgaacccacattttgcaggatttcattaacgttggttgaggttagaaaactggaactcgctttagttcgaggaatatataaatagatatggatatatatatatatatatatatatgagaatactctaagtactgataacaccatctgtacttgcggcgacatcagAGGTGTGCAGAATTGGCGACGACGCACCCGAGAATCAGAGCGACTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCTACTGGAAACCGCGCAAACCG------------
upper sequence: EFJ08057 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S1_447V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------------------------------------------------------------------gtatggaagaatttgtagcctctagactctagagcattccaacttc-tgcaagaatg-gtaaatctttgacaaaggttgggatcacagAGGATTGCG--CGAGCT--CGGCAGATCAGAGCGAGTGGTACTTCTTCAGCCACAAAGACAAGAAGTATCCGACCGGGAGCCGAACCAACAGGGCCACAACAGC
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gtaagaatcgatcagaatcctcggtgtactatgtatgacaccagactagaaaacacgtcctcacatgcttcgttgccccatttcagtctattaagattgaactcatggtgtgttcgagccctgggattgca-attagattccatgtccactacgtacacggacaagtaaccccgatgtggtcatcagAAGTGTGCAGGATTGGGGACGACCCACCAGAGAATCAAAACGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCCTCGGGCAATCGAGCGAACCG------------
upper sequence: EFJ08057 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S182_37V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------------------------------------------------------------gtatggaagaatttgtagcctctagactctag-agcattcca-acttctgcaagaatggtaaatctttg--acaaaggttgggatcacagAGGATTGCGCGAG-CTCGGCAGA---TCAGAGCGAGTGGTACTTCTTCAGCCACAAAGACAAGAAGTATCCGACCGGGAGCCGAACCAACAGGGCCACAACAGC
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gtaagcatcggaatcctgaaggtagtatggtgcagtgttcaacctcctcatctagtttcgtcaaaaaataaacatttaaaacagtactatccattgaattgtgatcaacataagctcaagagcatgttctcctcatctattgatagcatgaaatggtccagcagtattgacaaaaacttgttgcaccgatcagAAGTGTGCAGGATCGGGGACGACGCACCAGAGCATCAAAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAGTATCCCACAGGAAACCGTGCCAACCG------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagcattccaacttctgcaagaatggtaaatctttgacaaaggttgggatcacagAGGATTGCGCGAGCTCGGCAGATCAGAGCGAGTGGTACTTCTTCAGCCACAAAGACAAGAAGTATCCGACCGGGAGCCGAACCAACAGGGCCACAACAGC
ctttgac putative branch site (score: 4)
taaatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggaagaatttgtagcctctagactctagagcattccaacttctgcaagaatggtaaatctttgacaaaggttgggatcacagAGGATTGCGCGAGCTCGGCAGATCAGAGCGAGTGGTACTTCTTCAGCCACAAAGACAAGAAGTATCCGACCGGGAGCCGAACCAACAGGGCCACAACAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT