Sequence
atgc intronic sequence ATGC exonic sequencegttgtaatattttctctgttagttttggtcctttatagattcaattacatcttggttttgtgactttatagctttgctttctgatttttcagGTTATAAAAAACTCTAATGGTTGCAACCTAGCTGTTGATATATGGAGCCTTGGATGCACAGTTTTGGAAATGGCTACAACTAAACCTCCTTGGAGTCAGT
Basic information
species | Glycine max |
transcript | GLYMA16G30030.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os04g47240.3 (Oryza sativa), 3'ss of exon 8
-----gttgtaatattttctctgttagttttggtcctttatagattcaattacatcttggttttgtgactttata-gctttgctttctgatttttcagGTTATAAAAAACTCTAATGGTTGCAACCTAGCTGTTGATATATGGAGCCTTGGATGCACAGTTTTGGAAATGGCTACAACTAAACCTCCTTGGAGTCAGT
|| || ||| ||||| |||| | || || || || || ||| || | | | || ||| | ||||||||||||||||| ||||| ||||||||||||||||| |||||||| | |||||||| || |||| ||||||||| | ||||| || ||||| ||||
gtatcactgaaaatctttacttgttaattttt-tgtttcatgcat---atcttattgccatttctgtacatcacatactatgcaacaca--tacgcagGTTATAAAAAACTCAAATGGGTGCAACCTAGCTGTTGACATATGGAGTTTGGGATGCACTGTCCTGGAGATGGCTACATCGAAACCGCCATGGAGCCAGT
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 8
---------gttgtaatattttctctgttagttttggtcctttatagattcaattacatcttggttttgtgacttta-----tagctttgctttc-------------tgatttttcagGTTATAAAAAACTCTAATGGTTGCAACCTAGCTGTTGATATATGGAGCCTTGGATGCACAGTTTTGGAAATGGCTACAACTAAACCTCCTTGGAGTCAGT
| || | |||| | | | | | || || ||| | ||||| | | | || | | |||||| | | | | |||||||||||||| |||||||| || || || |||||||| ||||||||| | |||||||| ||||| || |||||||| | ||||| || ||||| || |
gtaatgaaaatcctacattcttctacacttctctagttatttgatgaatttatgcctatcttctctccgctGTTATAAAAATCAACCTTGCTTCTCTCACACATGTAATAACTATGCAGGTTATAAAAAATTCTAATGGATGTAATCTTGCTGTTGACATATGGAGCTTAGGATGCACGGTTTTAGAGATGGCTACCTCAAAACCACCATGGAGCCAAT
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G175504_T01 (Zea mays), 3'ss of exon 7
----------------gttgtaatattttct-ctgttagttttggtcctttatagattcaattacatcttggttttgtgactttatagctttgctttctgatttttcagGTTATAAAAAACTCTAATGGTTGCAACCTAGCTGTTGATATATGGAGCCTTGGATGCACAGTTTTGGAAATGGCTACAACTAAACCTCCTTGGAGTCAGT
|| || ||| | | || |||| | | | | || |||| | || || | | || | ||| | | |||||||||||||| |||||||| |||||||| | ||||| |||||||| | || ||||| || ||||||||||||| | || || || ||||| ||||
gtactgaaatgaagctcttcctttagtttgtatttttttttttaattcaatgtgcatcacattataatttctgttaacaaaatactaaccatgcagcacaaatg--cagGTTATAAAAAATTCTAATGGATGCAACCTTGTGGTTGACATATGGAGTTTAGGTTGCACTGTCCTGGAAATGGCTACCTCAAAGCCACCATGGAGCCAGT
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 8
--gttgtaatattttctctgttagttttggtccttta-tagattcaattacatcttggttttgtgactttatagctttgctttc-tgatttttcagGTTATAAAAAACTCTAATGGTTGCAACCTAGCTGTTGATATATGGAGCCTTGGATGCACAGTTTTGGAAATGGCTACAACTAAACCTCCTTGGAGTCAGT
|| | | | || ||| || | ||||| | || | || | | | |||| || | | || | | | | | |||||||||||||| ||| ||| || ||||| || |||||||||||||| | ||||||||||| | || |||||||| | ||||| || ||||| || |
gtattaccccaaatcttgcatt-gttctgctactttagttattttggccagatttatatatcctgacctt-tgcttatgttgtgacaaatatgcagGTTATAAAAAATGCTAGTGGATGTAACCTTGCAGTTGATATATGGAGTTTAGGATGCACAGTCCTAGAGATGGCTACTTCAAAACCACCATGGAGCCAAT
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 7
gttgtaatattttctctgt---tagttttggtcctttatagattcaattacatcttggttttgtgactttatagctttgctttctgattt-ttcagGTTATAAAAAACTCTAATGGTTGCAACCTAGCTGTTGATATATGGAGCCTTGGATGCACAGTTTTGGAAATGGCTACAACTAAACCTCCTTGGAGTCAGT
|| ||| |||| ||| || || ||| || || | | | ||| | | | ||| | || || | | || ||||||||||| || || |||||||||||||| ||||| ||||| ||||| || || |||||||||||||||||||| ||||| ||||| || ||||||||||
gtcagaatgttttttcttgccataaccttatctcttcatttat--gacaagcttttgatagtatttctt-acttctctgttcagttgttcgctcagGTTATAAGGAATTCAAATGGTTGCAACCTTGCTGTGGATATTTGGAGTCTAGGGTGCACAGTTTTGGAAATGGCCACAACAAAACCACCCTGGAGTCAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattcaattacatcttggttttgtgactttatagctttgctttctgatttttcagGTTATAAAAAACTCTAATGGTTGCAACCTAGCTGTTGATATATGGAGCCTTGGATGCACAGTTTTGGAAATGGCTACAACTAAACCTCCTTGGAGTCAGT
ttctgat putative branch site (score: 3)
ctttctgatttttc CT-rich tract
aattacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgtaatattttctctgttagttttggtcctttatagattcaattacatcttggttttgtgactttatagctttgctttctgatttttcagGTTATAAAAAACTCTAATGGTTGCAACCTAGCTGTTGATATATGGAGCCTTGGATGCACAGTTTTGGAAATGGCTACAACTAAACCTCCTTGGAGTCAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG