Sequence
atgc intronic sequence ATGC exonic sequencegtcttttttcctctccttgtttttgttatattataatcaaagctgaagttaatagtcttacagCTTCTTTTATTGTTACTCAGAGGAGTACATTGGGTTAGATGAAAACAAATATATTGGGGATCTCCTGGTGGAATTCAAAGCTGCAAAGGATCGAAGTAAA
Basic information
species | Glycine max |
transcript | GLYMA09G32740.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 5
gtcttttttcctctccttgttttt---gttatattataatcaaa----gctgaagttaatagtcttacagCTTCTTT--TATTGTTACTCAGAGGAGTACATTGGGTTAGATGAAAACAAATATATTGGGGATCTCCTGGTGGAATTCAAAGCTGCAAAGGATCGAAGTAAA--------------------
|| ||| || | | | | | || || | || | || |||| || | | ||| || | || ||| |||||||||||||||| |||||||| |||||||||||||| || ||||| |||||||| || || |||||||| | |||
gtatttctttcagtacaaagtcacaaggctaccttttcctccctttctgttgtttttaacagcacttttgtttccttacttttcatacacagAGGAGTACATTGGTTTAGATGATAACAAATATATTGGTGACCTCCTATCTGAATTCAAGGCAGCCAAGGATCGGAACAAAGGAGAAATTTTACACTGCAA
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 6
--------------------------------------------gtcttttttcctctccttgtttttgttatattata-atcaaagctgaagttaatag--tcttacag-
| | | |||| ||| || |||| | | || | || || ||| | || || || ||||| || | ||||||| |||||||| |||||||| |||||||||||||| || | || ||||||| | | || |||||||| | |||
gtaactagcaagtcatattctttttttcccttttctatttcataatttaaataatcctccatgtggtttggatatcaaggagcagaaagaaatgtattaggattttgtagatgtttttcaagtaacatgtgcttttctttatcttttatatgcagAGGAATACATTGGATTAGATGATAACAAATATATTGGTGACTTGCTATCTGAATTCAGATCAGCTAAGGATCGCAACAAAGGAGAAATTCTTCATTGCAA
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------------gtcttttttcctctccttgtttttgtt-atattataatcaaagctgaagttaatagtcttacagCTTCTTTTATTGTTACTCAGAGGAGTACATTGGGTTAGATGAAAACAAATATATTGGGGATCTCCTGGTGGAATTCAAAGCTGCAAAGGATCGAAGTAAA--------------------
|| | | | || || || || ||| | |||| | | | ||| | | || | | ||||||| |||||||| |||||||| |||||||||||||| || | || ||||||||| | || |||||||| | |||
gtaattaccaatccatattgttttttcttttctatttcttaatttaattaatgcatgtggtttggatatcatggagcaggaggaaacataggtggattttgtagaaaaatttcaagtaacacggtgcatttctttatcttttat-atgcagAGGAATACATTGGATTAGATGATAACAAATATATTGGTGACTTGCTATCTGAATTCAAATCAGCTAAGGATCGCAACAAAGGAGAAATTCTTCATTGCAA
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 6
------gtcttttt-tcctctccttgtttttgttatattat----aatcaaagctg--aagttaatagtcttaca-gCTTCTTTTATTGTTACTCAGAGGAGTACATTGGGTTAGATGAAAACAAATATATTGGGGATCTCCTGGTGGAATTCAAAGCTGCAAAGGATCGAAGTAAA--------------------
|||| || || ||| | |||| || |||| | ||||| | || ||| | | | | || |||| || |||| ||||||||| ||||| |||||||| |||||||||||||||||| | ||| ||||||||| || ||||||||| ||||||||
gtatccatcttattatcttctggattattttattttatttttttaaatcagactcactaaattagtcatttgatgtgcactttttctttttacatagAGGAGTATATTGGATTAGATGATAACAAATATATTGGGGATTTATTGGCGGAATTCAAGGCAGCAAAGGATAGAAGTAAAGGAGAAATTTTGCATTGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctctccttgtttttgttatattataatcaaagctgaagttaatagtcttacagCTTCTTTTATTGTTACTCAGAGGAGTACATTGGGTTAGATGAAAACAAATATATTGGGGATCTCCTGGTGGAATTCAAAGCTGCAAAGGATCGAAGTAAA
agttaat putative branch site (score: 4)
ttgtttttgttatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcttttttcctctccttgtttttgttatattataatcaaagctgaagttaatagtcttacagCTTCTTTTATTGTTACTCAGAGGAGTACATTGGGTTAGATGAAAACAAATATATTGGGGATCTCCTGGTGGAATTCAAAGCTGCAAAGGATCGAAGTAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG