Sequence
atgc intronic sequence ATGC exonic sequencegtaccttagaatcttttgctcgtttgaaatgtttttcttgtggtttacctttctagtcgatcgattttcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ16113 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ16113 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os04g36610.1 (Oryza sativa), 3'ss of exon 1
-----gtaccttagaatcttttgctcgtttgaaatgtttttcttgtggtttacctttctagtcgatcgattttcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT
|| | | | | | | | |||| ||| | || || | | | | | |||| || ||||| | ||||| || ||||||||||| ||||||||||||||||| || ||||||||||||||||||| ||| ||||||||||| |||| ||||| |
gtacggttcttcatggcatctgctccctcccgtgtgttgaccttttagtcaacgtgttgacctg--tggttttgactttgtggcagGTTGACCTCACCGGCGGCTACTACGACGGCGGCGACAACGTCAAGTTCGGGTTCCCGATGGCGTTCACGACGACGATGCTGTCGTGGGGCGTCGTGGAGT
upper sequence: EFJ16113 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os08g29770.1 (Oryza sativa), 3'ss of exon 1
------gtaccttagaatcttttgctcgtttgaaatgtttttcttgtggtttacctt-------tctagtc----gatcgatt--ttcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT
|| |||| | || | || ||| | || || | || | | | | || |||| ||| || || ||||||||| || || || ||||||||||| | ||||||||||||||||| || | |||||||||||||||| | || |||||| ||||||| || || |
ttaaaaaaacggaagaagcattgatcaatggaaagagttcatattatgtctctccatggataaatatgattttggtatggattaattcaatggtggtcagGTGAACCTGACCGGCGGCTACTACGACGCCGGCGACAACGTCAAGTTCGGGTACCCGATGGCGTTCACGGTGACCCTGCTGGGCTGGAGCGCCGTCGAGT
upper sequence: EFJ16113 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os06g14540.1 (Oryza sativa), 3'ss of exon 1
------------------------------------gtaccttagaatcttttgc---tcgtttgaaatgtttttcttgtggtttac---ctttctagtcgatcgattttcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT
| ||| ||||| | | |||| | ||| | | || | | | | | | || || |||||| | || |||||||| |||||||| | ||||||||||| ||||| || |||||||||||||||||| ||||| |||||||| | || | || |
gtacggaccaccaccgctctctctctctctctgttctagcattaatgcggtttgcaatgtagtagtaatgatgacgatgtcgctgacggtttcttggaatggtggcgtggcgtggcgtggcagGTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGGCTGATCGACT
upper sequence: EFJ16113 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os02g50040.1 (Oryza sativa), 3'ss of exon 1
----gtaccttagaatcttttgct---cgtttgaaatgtttttcttgtggtttacctttctagtcgatcgattttc-gctgctgct-----cagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT
||| | | || | || |||| ||||| | || ||| | | || | | | | | |||| || ||||| | | || ||||| |||||||| | ||||||||||| ||||| || |||||||||||||||||| |||||| |||||||| | || | || |
gtacgtattctcgt-cctataacttggcgttaagaatgtactactggtgaagcagcattgtgatttgtgagtaacctgctgtggccgcgtgtagGTGGACTTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTGATGTCGTGGGGGCTGATCGACT
upper sequence: EFJ16113 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os01g21070.1 (Oryza sativa), 3'ss of exon 1
--------------------------------------------gtaccttagaatcttttgctcgtttgaaatgtttttcttgtggtttacctttctagtcg-atcgattttcgc---tgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT
| | | ||| | ||| | | | | ||| | | | | ||| || | || || || |||||||| | | |||||| |||||||| | ||||||||| | ||||| || |||||| ||||||||| || ||| ||||| |||||||||||||||| |
gcaagaaactctccgctcctccgcgtttcaccatttcgtcggcattggcgccgtctctctctctctctctctctctctctctctctctctctcgccatggtctcatggcttgatgcgtttgtctctcagGTGGACTTGGTGGGAGGGTACTACGACGCCGGCGACAACATGAAGTTCGGGTTCCCGCTGGCGTTCAGCATGACGATGCTGGCGTGGAGCGTGGTGGAGT
upper sequence: EFJ16113 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os08g02220.1 (Oryza sativa), 3'ss of exon 1
gtaccttagaatcttttgctcgtttgaaatgtttttcttgtggtttacctttctagtcgatcgattttcgc-----tgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT
|||| | | | | | ||| || | | || ||||| | |||| || || ||||||| || | ||| || |||||||| | ||||||||||||||||| ||| | || ||||||||| ||| ||| ||||| ||||||||||| | || |
gtacgtacgccgcctct-ctctctttccctttcttccttgtctccggcgaggaggagtttgtgattccggcgtgtttgtgtttcagGTGGATTTGGTGGGCGGGTACTACGACGCCGGCGACAACGTCAAGTTCGGCCTGCCCATGGCGTTCTCGACGACGATGCTGGCGTGGAGCGTGCTCGACT
upper sequence: EFJ16113 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G125436_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------------------------gtaccttag--aatcttttgctcgtttgaaatgtttttcttgtggtttacctttctagtcgatcgattttcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT
|||| | | || ||| | | | ||| | | | | ||| | || | ||| || ||||| | ||||| || || |||||||| |||||||||| |||||| |||||||||||||| ||||||| ||| ||||||||||||||||| ||||
gtacgtacttccttcctgctgtgtcttgttcgaaaacatgggtcagcgcgctgacggctgacggctgacctgacctgacctggggcttggactggacctggaccttcttagtctctctatctgtctgttgacgtgcgc-gcgcggcagGTCGACCTCACCGGCGGGTACTACGACGGCGGCGACAACGCCAAGTTCGGCTTCCCGATGGCCTTCACGACGACGATGCTGTCGTGGAGCGTGCTGGAGC
upper sequence: EFJ16113 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G331566_T02 (Zea mays), 3'ss of exon 1
----------------------------gtaccttagaatcttttgctcgtttgaaatgtttttcttgtggtttacctttctagtcgatcgattttcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT
||| | || | | | |||||| ||| | | || | | | | || | || | |||||| | || ||| || ||| |||| | || |||||||||||||| || |||||||||||||||| || ||| ||||| |||||||||||||||| |
gtaagtactccctagcgtggaggttatgtcaccggacggcctctctgctttcagtcctgttttatctgttgatggccggcgttcttgttgaatgtg---tggcgggcagGTGGACCTGGTGGGCGGGTACCACGACGCTGGTGACAACGTCAAGTTCGGGTTCCCGATGGCGTTCAGCATGACGATGCTGGCGTGGAGCGTGGTGGAGT
upper sequence: EFJ16113 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
---------------------------------gtaccttagaatcttttgctcgtttgaaatgtttttcttgtggtttacctttctag------tcgatcgattt--tcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT
| || | | | | | | | || | | || | | | || | |||| ||| || |||||| |||| || ||||| |||||||| | ||||||||||| ||||| || |||||||||||||||||| ||||| |||||||| || || | || |
gtacgtgcaccgacccagtccgactaataaatcactctctatagttgccttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
upper sequence: EFJ16113 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G009025_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------------gtacctta---gaatcttttgctcgtttgaaatgtttttcttgtggt-------ttacctttctagtcgatcgattttcgc-tgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT
|| ||| | | | | ||| | | | | |||| | || ||| || | || | | |||||| | || ||| || |||||||| | ||||||||||||||||| ||| | || ||||||||||| | |||| ||||| |||||||||||| |||
gtaataatgcttctacctcctgctatagtgtatagaaacagcatggagtagtagtctcttgctcgcactgtccacgtccacgaaggcaccgatgggcgatggccacctcacctcgattgtacatctatatccggacggagtgcagGTGGACCTGGTGGGCGGGTACTACGACGCCGGCGACAACGTCAAGTTCGGCCTGCCCATGGCGTTCACCACCACGATGCTGGCGTGGAGCGTGGCGGACA
upper sequence: EFJ16113 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G167669_T01 (Zea mays), 3'ss of exon 1
-----------gtaccttagaatcttttgctcgtttgaaatgtttttcttgtggtttacctttctagtcgatcg-attttcgctgctgctc-------agGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT
| || |||| || || ||| | | || || | ||| | ||| |||||||| ||||||| | ||||| ||||||||||| | || |||||||||||||| || |||||||||||||||| |||| || ||| ||||||| || || |
ggacctttttgacaatttttttcttttttctttttcaaaaagaaagaaggaagaattgaagctcattgtgttcgtgtcgtcgttgctgctccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGTTTCCCGATGGCGTTCAGCGTCACCCTCCTGAGCTGGAGCGCCGTCGAGT
upper sequence: EFJ16113 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA08G04840.1 (Glycine max), 3'ss of exon 1
----gtaccttagaatcttttgctcgtttgaaatgttt---ttcttgtggtttacctttctagtcgatcgattttcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT
|| ||| | || || | | | || | || | | | | || | ||| | | |||||||| | | | ||||| |||||||| | || || ||| | ||||| || || |||||||||||||||| ||| ||||||||||||||||| | || |
gtaagtttcttgttctgttatgaaaatgtagattgatagagaatatgatgatgattaatgaggtaggcacattgtgttgtttactcagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGGTTTCCGATGGCGTTCACGACGACGATGCTGTCGTGGAGCGTGATCGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatgtttttcttgtggtttacctttctagtcgatcgattttcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT
ttttcgct CT-rich tract
tttttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaccttagaatcttttgctcgtttgaaatgtttttcttgtggtttacctttctagtcgatcgattttcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA