Sequence
atgc intronic sequence ATGC exonic sequence...ctttgttacattttatatgcttctttcctgactgcatatagtggcttgtacttttccttatcatctttgtaattgtatgactttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCAAAAGGAGTTTTGCTTGTTGGTCCACCTGGCACTGGAAAAACTATGTTAGCAAGAGCTATTGCTGGAGAGG
Basic information
species | Glycine max |
transcript | GLYMA14G10950.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g39260.1 (Oryza sativa), 3'ss of exon 5
ctttgttacattttatatgcttctttcctgactgcatatagtggcttgtacttt-tccttatcatctttgta-attgtatgact---------ttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCAAAAGGAGTTTTGCTTGTTGGTCCACCTGGCACTGGAAAAACTATGTTAGCAAGAGCTATTGCTGGAGAGG
| | || || || | | | | || | | | | |||| | || || || | | | |||| | | ||||| ||||| ||||||||||| || || |||||||| || ||||| |||||||| |||||||||||||| || ||||||||||| ||||||||||| || |
-----------tatgcatcgttaagcccataaatggtgtgaggatttacccctcattttcatcacatgcatatgttatacggcaaatgacaagctgcttccttgttttcagCGTTTTACACGTCTTGGTGGAAAACTGCCAAAAGGTGTCTTGCTGGTTGGTCCTCCTGGCACTGGAAAGACCATGTTAGCAAGGGCTATTGCTGGGGAAG
upper sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g39250.1 (Oryza sativa), 3'ss of exon 5
---ctttgttacattttatatgcttc-tttcctgactgcatatagtggcttgtacttttcct-tatcatctttgtaattgtatgactttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCAAAAGGAGTTTTGCTTGTTGGTCCACCTGGCACTGGAAAAACTATGTTAGCAAGAGCTATTGCTGGAGAGG
|||| | ||| | || || |||| | |||| | | | | | ||||| | || ||| | | || | || | ||| | ||||| ||||||| ||||||||| || || |||||||| || ||||| ||||| || ||||||||||| || || |||||||| || ||| ||||||| || |
gcactttaatgcatatatgatctatcatttcataactgttttt---gtcatatacttgtgctatatggtgatcagaagtcacaagctgcctccttctttt--cagCGTTTTACTCATCTTGGTGGAAAACTGCCAAAAGGTGTCTTGCTGGTTGGCCCTCCTGGCACTGGGAAGACCATGTTAGCGAGGGCTGTTGCTGGGGAAG
upper sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G096764_T01 (Zea mays), 3'ss of exon 5
ctttgttacattttatatgcttctttcctgactgcatatagtgg---cttgtacttttccttatcatctttgtaattgtatgactttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCAAAAGGAGTTTTGCTTGTTGGTCCACCTGGCACTGGAAAAACTATGTTAGCAAGAGCTATTGCTGGAGAGG
|| | | | | | || |||| || | | || ||| | || || || | | | || | | | | | | | |||||||| || ||||||||||| || ||||| |||||||| |||||||||||||| ||||||||||| ||||| ||| |||| || ||||||||||| || |
---tgcttttatgaagctcatctcgtcttgacaacacctggaggtaccttatttttcattttgtctttcgtatgatgctcacaaactgtgctcttgttttcagCGCTTCACACGTCTTGGTGGAAAACTTCCGAAAGGAGTCTTGCTTGTTGGTCCTCCTGGCACTGGGAAAACCATGCTAGCTAGGGCTATTGCTGGTGAAG
upper sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G451483_T01 (Zea mays), 3'ss of exon 6
ctttgttacattttatatgcttctttcctgactgcatatagt-ggcttgtacttttccttatca----tctttgtaattgtatgactttttttcccttgtgac-agCGCTTTACTCGTCTTGGTGGTAAGCTTCCAAAAGGAGTTTTGCTTGTTGGTCCACCTGGCACTGGAAAAACTATGTTAGCAAGAGCTATTGCTGGAGAGG
|| | ||| || | || | ||| || | || ||||| || | ||| | | || | | | | || | ||||| | |||| ||||| | |||||||| |||||||| ||||| |||||||| || || |||||||| ||||||||||||||| | ||||| ||||| ||||| || |
-----ttgcgctttttagggacacgtca-aagtgctcatttttgggttgtatattcatgtttcaaatattagtatagtactcacattcacctttcattgtgcccagCGTTTTACATGCCTTGGTGGAAAGCTTCCTAAAGGTGTTTTGCTGGTGGGACCACCTGGAACTGGAAAAACTATGCTGGCAAGGGCTATAGCTGGGGAAG
upper sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G463032_T01 (Zea mays), 3'ss of exon 4
ctttgttacattttatatgcttctttcctgactgcatatagtggc-ttgtact--tttccttat-catctttgtaat-tgtatgactttttttcccttgtga-cagCGCTTTACTCGTCTTGGTGGTAAGCTTCCAAAAGGAGTTTTGCTTGTTGGTCCACCTGGCACTGGAAAAACTATGTTAGCAAGAGCTATTGCTGGAGAGG
||| ||||| || | | | | | | | | ||| | ||||| | | |||| | ||| ||| || | | | ||| | |||||||| || |||||||||| || ||||| ||||| || |||||||| || || ||||||||||| ||||| ||| |||| || ||||||||||| || |
------accatcaaatatgattgtgtgccgtcgtaacacacgggcatcgtactagtcttattatatgtttttataagatgctcacaaactgtgctcttattttcagCGCTTCACATGTCTTGGTGGAAAACTTCCTAAAGGTGTCTTGCTTGTGGGCCCTCCTGGCACTGGGAAAACCATGCTAGCTAGGGCTATTGCTGGTGAAG
upper sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G26140.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------------------------------ctttgtta---cattttatatgcttctttcct---gactgcatatagtggcttgtactt-------ttccttatcatctttg----taattgtatgactttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCAAAAGGAGTTTTGCTTGTTGGTCCACCTGGCACTGGAAAAACTATGTTAGCAAGAGCTATTGCTGGAGAGG
||| | || |||| | | | |||| | | | | | || | || | | | | | || | | | | | | |||| | || | || | || |||||||| || || |||||||| || || || |||||||| ||||| ||||| || |||||||||||| | || ||||||||||||||||| |
gtaaattcacagtgctagagtgtttttctagttaagtataaaatctgtctagtgatgtaaattcaaaagcataaatcatgtgaagttatcatatagacctttatcctctgaattatctgtgccaggtttttctagagttagtactgttttgttcttaggcctcactctttcatcttttgatctttactatagAGGTTCACTCGTCTGGGAGGAAAGCTTCCTAAGGGTGTGTTGCTTGTCGGTCCTCCTGGGACAGGAAAAACTATGCTTGCTAGAGCTATTGCTGGAGAAG
upper sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 5
-----ctttgttacattttatatgcttctttcctgactgcatatagtggcttgtactttt---ccttatcatctttgtaattgtatgactttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCAAAAGGAGTTTTGCTTGTTGGTCCACCTGGCACTGGAAAAACTATGTTAGCAAGAGCTATTGCTGGAGAGG
||| | | || | ||| | ||||| | ||| || | || | || | | ||| | ||| |||| |||||||||| ||||||||| |||||||| ||||| || |||||||| || |||||||||||||||||||||||||| || || || ||||| ||||||||||| |||||||| |
aaaaacttccatgaaattaaaatg--taaaccctgaagccctatctctagttagagttgtatatctgaataggtttcttattttatg------tttcccttgttacagCGCTTCACTCGTCTAGGTGGCAAACTTCCAAAGGGTGTTTTGCTTGTTGGTCCACCTGGCACCGGCAAGACCATGTTGGCAAGAGCTATCGCTGGAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtacttttccttatcatctttgtaattgtatgactttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCAAAAGGAGTTTTGCTTGTTGGTCCACCTGGCACTGGAAAAACTATGTTAGCAAGAGCTATTGCTGGAGAGG
ctttttttcccttgt CT-rich tract
tttgtaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttgttacattttatatgcttctttcctgactgcatatagtggcttgtacttttccttatcatctttgtaattgtatgactttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCAAAAGGAGTTTTGCTTGTTGGTCCACCTGGCACTGGAAAAACTATGTTAGCAAGAGCTATTGCTGGAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - -tgcttct
- - - - - - - - - - - - -tcctgac
- - - - - - - - - - - - - - - - tgcatat
- - - - - - - - - - - - - - - - - - - - gtggctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatga