Sequence
atgc intronic sequence ATGC exonic sequence...tcgtgattgatcgaaaatcaaatcaaacgttaggactacatatgctttttttgtgtgtagggtgtgttgcttatacttaattccttcttgcactgtaaagGTTGCAAGTTGGGGTGCTTACCTTTTGAAAAGAGACATCATAGCTATGTCCTTTGCACCAAGAGATACACATGAAGCACAGGTCCAGTTTGCATTGGAAA
Basic information
species | Glycine max |
transcript | GLYMA05G36550.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G36550.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g01450.1 (Oryza sativa), 3'ss of exon 2
tcgtgattgatcgaaaatcaaatcaaacgttaggactacatatgctttttttgtgtgtagggtgtgttgcttatacttaattccttcttgcactgtaaagGTTGCAAGTTGGGGTGCTTACCTTTTGAAAAGAGACATCATAGCTATGTCCTTTGCACCAAGAGATACACATGAAGCACAGGTCCAGTTTGCATTGGAAA
|||| |||| | | | | ||| | | | |||||| | | | ||| ||| | | ||| |||| ||||||||||| ||||| ||| | || || ||||||| ||||||| |||||||| |||||| ||||||| ||||| || ||||||||||||||
--gtgagtgatttagcaatttccaagatattatgtgtttctgcaaattttttaggatttatgaatgtatcttggatgttgttc---------------agGTGGCAAGTTGGGGCGCTTATCTTATTAAGAGGAACATCATCACTATGTCATTTGCACCTAGAGATTCACATGAGGCACAAGTGCAGTTTGCATTGGAGC
upper sequence: GLYMA05G36550.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G164916_T03 (Zea mays), 3'ss of exon 3
tcgtgattgatcgaaaatcaaatcaaacgttaggactacatatgctttttttgtgtgtagggtgtgttgcttatacttaattccttcttgcactgtaaagGTTGCAAGTTGGGGTGCTTACCTTTTGAAAAGAGACATCATAGCTATGTCCTTTGCACCAAGAGATACACATGAAGCACAGGTCCAGTTTGCATTGGAAA
|||| ||| || | | ||| | | ||| | || || || | | ||| | | ||| | || | |||| ||| |||||||||| ||||||||||| ||| |||| || ||||||| | ||||| ||||| ||||| ||| ||||||| |||||||| ||||||||||| ||
--gtgagtgaccgga---ccaatgtttctatgatactgtctgtgattccttctc----aaaatttgtggatgatagt--atctttgcttgtg-tgtgcagGTTGCAAGCTGGGGTGCTTATCTTATGAATAGGAACATCATCACCATGTCTTTTGCGCCAAGGGATTCACATGAGGCACAGGTACAGTTTGCATTAGAGC
upper sequence: GLYMA05G36550.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G10440.1 (Arabidopsis thaliana), 3'ss of exon 1
tcgtgattgatcgaaaatcaaatcaaacgttaggactacatatgctttttttgtgtgtagggtgtgttgcttatacttaattccttcttgcactgtaaagGTTGCAAGTTGGGGTGCTTACCTTTTGAAAAGAGACATCATAGCTATGTCCTTTGCACCAAGAGATACACATGAAGCACAGGTCCAGTTTGCATTGGAAA
|| | || | | | | | | |||| ||| ||| |||| | ||| || | | ||| || || | | | ||||||||||| ||||||||||| ||||| |||||||| || ||| |||| ||||| |||||||| || |||||||| ||||| |||||||| || |||
--gtaagtgtttcattgtaagagtatacgt---------atacacttctttttgat--------cattgtttg-attcaatatctgttttttatatta-gGTTGCAAGTTTTGGTGCTTACCTCTTGAAGAGAGACATTATGGCTGTGTCTTTTGCTCCAAGAGACACTCATGAAGCTCAGGTACAGTTTGCTTTAGAAC
upper sequence: GLYMA05G36550.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv02s0025g03200.t01 (Vitis vinifera), 3'ss of exon 1
-----------tcgtgattgatcgaaaatcaaa---tcaaacgttaggactacat-atgctttttttgtgtgtagggtgtgttgcttatacttaattccttcttgcac-tgtaaagGTTGCAAGTTGGGGTGCTTACCTTTTGAAAAGAGACATCATAGCTATGTCCTTTGCACCAAGAGATACACATGAAGCACAGGTCCAGTTTGCATTGGAAA
| | | | || | | | ||| | | | | ||| || || | || |||| ||| | ||| ||| ||||||||||| |||||||| ||| | || ||||| || || | |||||||| |||||||||||||| |||||||||||||||||||||||||| | ||
gtaagtaaaggcttcaactccttgtccatttaggccttctatattaccattgttttgtagtttattgcagtagctaacaggagtctcctact-gtttcttgattgggtgtgttaagGTTGCAAGCTGGGGTGCCTACTTGTTAAAAAGGGATATTCTGGCTATGTCTTTTGCACCAAGAGACACACATGAAGCACAGGTCCAGTTTGCCCTAGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttttgtgtgtagggtgtgttgcttatacttaattccttcttgcactgtaaagGTTGCAAGTTGGGGTGCTTACCTTTTGAAAAGAGACATCATAGCTATGTCCTTTGCACCAAGAGATACACATGAAGCACAGGTCCAGTTTGCATTGGAAA
acttaat putative branch site (score: 4)
ttccttcttgcact CT-rich tract
ttatacttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcgtgattgatcgaaaatcaaatcaaacgttaggactacatatgctttttttgtgtgtagggtgtgttgcttatacttaattccttcttgcactgtaaagGTTGCAAGTTGGGGTGCTTACCTTTTGAAAAGAGACATCATAGCTATGTCCTTTGCACCAAGAGATACACATGAAGCACAGGTCCAGTTTGCATTGGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- gtgattg
- - - - - - gaaaatc
- - - - - - - - - - - - - - - - - - - catatgc
- - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttat