Sequence
atgc intronic sequence ATGC exonic sequence...cacagtgtatgtggattatttatagccaagttaccttttcatattattattgttttaatttgacatgtaggtagtaaatatccactgttttatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTTTACTGGCAAAGGCTGTGGCAGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTTGTAGAGT
Basic information
species | Glycine max |
transcript | GLYMA14G37090.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G37090.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 4
cacagtgtatgtggattatttatagccaagttaccttttcatattattattgtt-ttaatttgacatgtaggtagtaaatatccactgttttatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTTTACTGGCAAAGGCTGTGGCAGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTTGTAGAGT
| | ||| | | | || || | |||| | | | | ||| || || | | |||| ||||||||||| ||||| || || || ||||| | || ||||| ||||| |||||||||||||| || ||||| |||||||| ||||| ||||| ||||| ||||
-----------------gtcagttctgcagtcatttaagta-atgatgaatgttgctggactagagtttttgtactatg-atgtaattcattat-ttacagGTGGGCCTTCCAGGAACTGGAAAGACGCTTCTTGCAAAAGCTGTCGCAGGGGAAGCTGAAGTCCCATTCATAAGTTGCTCTGCAAGTGAATTTGTGGAGT
upper sequence: GLYMA14G37090.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G072865_T05 (Zea mays), 3'ss of exon 4
--------------cacagtgtatgtggattatttatagccaagttaccttttcatattattattg----ttttaatttgaca----tgtaggtagtaaatatccactgttttatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTTTACTGGCAAAGGCTGTGGCAGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTTGTAGAGT------------
| | | |||| | || | | | | | | ||| || || | |||||| ||| || | || | | ||| ||| ||||||||||||||| ||||| || ||||| | || ||||| || || ||||| ||||| || || ||||| |||||||| ||||||||||| ||||| |||
ttcgtctcggtgctcgccctcctcgtggtgtcttattggttggttctgcaaatgcttttagtaatggaaactactgcttgacaattgtgtttgttaccataatgtaattctttctct-acaggtgggtcttccagggactggaaagacacttcttgcaaaagccgtagcaggagaagcagaagTCCCATTCATAAGTTGCTCTGCTAGTGAATTTGTTGAGCTATATGTAGGCA
upper sequence: GLYMA14G37090.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G072865_T01 (Zea mays), 3'ss of exon 4
cacagtgtatgtggattatttatagccaagttaccttttcatattattattgttttaatttgacatgtaggtagtaaatatccactgttttatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTTTACTGGCAAAGGCTGTGGCAGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTTGTAGAGT
|| || | | | | | | || || || | | ||| || | || | | ||| ||| ||||||||||||||| ||||| || ||||| | || ||||| || || ||||| ||||| || || ||||| |||||||| ||||||||||| ||||| |||
--------------gttggttctgcaaatgcttttagtaatggaaactactgcttgacaat--tgtgtttgttaccataatgtaattctttctct-acagGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGCAAAAGCCGTAGCAGGAGAAGCAGAAGTCCCATTCATAAGTTGCTCTGCTAGTGAATTTGTTGAGC
upper sequence: GLYMA14G37090.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G163193_T02 (Zea mays), 3'ss of exon 4
cacagtgtatgtggattatttatagccaagttaccttttcatattattattgttttaatttgacatgtaggtagtaaatatccactgttttatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTTTACTGGCAAAGGCTGTGGCAGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTTGTAGAGT
|| || | | | || | | |||| || || | | | | | || | || | | ||||||| ||||||||||||||| ||||| || ||||| | || ||||| || || ||||| ||||| || || || || |||||||| ||||||||||| ||||| |||
--------------gttggttttgcaaatgctatcagtaatggcaattactgcttgacaattgtgttt-gttaccatattgttatt-ctttatct-acagGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGCAAAAGCCGTAGCAGGAGAAGCAGAAGTCCCGTTCATAAGTTGCTCTGCTAGTGAATTTGTTGAGC
upper sequence: GLYMA14G37090.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------cacagtgtatgtggattatttatagccaagttaccttttcatattattattgttttaatttgacatgtaggtagtaaatatcc-actgttttatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTTTACTGGCAAAGGCTGTGGCAGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTTGTAGAGT
||| | | | |||| |||| | | ||| | || | || | | | | | || | ||| ||| | || ||||| |||||||| || ||||| || || | || ||||||||||| || ||||||||||| || || || |||||||| ||||| |||||||||||||||
gtgagttttatcatttgatttcactttattcttatattacgtatat----atcatggtttaacgtt-tggttacaagagctctcctttagaatgatatgcctttgactcctttcttttccagGTTGGTCTTCCCGGAACAGGGAAAACCCTTCTTGCAAAGGCTGTTGCTGGGGAAGCTGAAGTCCCCTTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGC
upper sequence: GLYMA14G37090.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 4
--------cacagtgtatgtggattatttatagccaagttaccttttcatattat---tattgttttaatttgacatgtaggtagtaaatatccactgttttatctta-cagGTGGGTCTTCCTGGGACAGGTAAGACTTTACTGGCAAAGGCTGTGGCAGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTTGTAGAGT
| | |||| | | | |||| |||| || | | |||| | ||||| | | | ||| || | | | | | || |||| ||||||||||| ||||| || || | || ||||| ||||| || |||||| ||||||| ||||| |||||||| ||||| |||||||||||||||
gtgagtttaataatgtagttaca--acttatggcca--tttcttaggtggtttatgcgcaatgtttggttactatctttagaatttatggctttatttccctgttttggtagGTCGGTCTTCCTGGAACAGGGAAAACCCTTCTTGCAAAAGCTGTTGCTGGGGAATCTGATGTTCCATTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGC
upper sequence: GLYMA14G37090.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 4
------cacagtgtatgtggattatttatagccaagttaccttttcatattattattgttttaatttgacatgtaggtagtaaatatccactgttttatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTTTACTGGCAAAGGCTGTGGCAGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTTGTAGAGT
| | || | ||| | || |||| || || | | | || | || || | | | | |||| || | ||||||||||||||||||||||||||||||||||||| | || |||||||||||||| ||||| ||||| ||||| ||||||||||||||||| |||||||||||||| |
ctaccaaagaacagatacaagtggtttcca--taatttactcttggatgtaagtttttatgta---tggc-tttgatttgtaagtacggctttggctatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTCTCCTAGCAAAGGCTGTGGCTGGGGAGGCTGAAGTGCCTTTTATAAGTTGTTCTGCAAGTGAGTTTGTAGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attattgttttaatttgacatgtaggtagtaaatatccactgttttatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTTTACTGGCAAAGGCTGTGGCAGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTTGTAGAGT
ttttatctt CT-rich tract
ttttaatttgacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cacagtgtatgtggattatttatagccaagttaccttttcatattattattgttttaatttgacatgtaggtagtaaatatccactgttttatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTTTACTGGCAAAGGCTGTGGCAGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTTGTAGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - -tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccactg