Sequence
atgc intronic sequence ATGC exonic sequence...tatcgtgttgttctgaaatttacaacatggtaaagtcaagtttattgttgttccctgggtagctagtttgttgatttcactctacctttggcatgcttagATGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTAGAGGAAGAGGTAGCCATGTTTTGCCCCATGATATGCCAGGAAGTACTTC
Basic information
species | Glycine max |
transcript | GLYMA16G30080.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G30080.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g01660.1 (Oryza sativa), 3'ss of exon 2
-----------------tatcgtgttgttctgaaatttacaacatggtaaagtcaagtttattgttgttc--cctgggtagctagtttgttgatttcactctacctttggcatg--ctta-----gATGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTAGAGGAAGAGGTAGCCATGTTTTGCCCCATGATATGCCAGGAAGTACTTC
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gtatgacccctatgcatttctagatcataactattttttctgtttattggaggggaaacaattgttctccagccttatcagctattcatttggttccaatttaatttcattgtgaactcacagGCGTTGAAGAGTTATATTTGGCTTCAGTGCTTTGATGGTTCCATACAACAAGTGGAGGAGGAGGTTGCCATGTTTTGCCCTATGATATGTCGAGAGATAG---
upper sequence: GLYMA16G30080.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G109725_T04 (Zea mays), 3'ss of exon 3
tatcgtgttgttctgaaatttacaacatggtaaagtcaagtttattgttgttccctgggtagctagtttgttgatttcactctacctttggcatgcttagATGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTAGAGGAAGAGGTAGCCATGTTTTGCCCCATGATATGCCAGGAAGTACTTC
|| | | || | || | || || | | ||| || || || ||| | ||| ||| | | || | || ||||||||||| | |||||||| ||||||||||| ||||| ||||| || ||||| |||||||||||||| | ||| |
----gtaattagagggaagcaattacttttccaa-tcttatgcggttcaattcagcctgtcttgagcttattggtggtgaactataacagGCGT-------TAAAGACTTATATCTGGCTTCAGTGCTTTGATGGTTCCATTCAGCAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCGTGAAATTG---
upper sequence: GLYMA16G30080.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G109725_T03 (Zea mays), 3'ss of exon 2
------tatcgtgttgttctgaaattta-caacatggtaaagtcaagtttattgttgttccctgggtagctagtttg--ttgatttcactctacctttggcatgcttagA-------TGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTAGAGGAAGAGGTAGCCATGTTTTGCCCCATGATATGCCAGGAAGTACTTC
| | || | | | || | | ||| | || || | | || || || | || ||| || | | || | || ||||||||||| | |||||||| ||||||||||| ||||| ||||| || ||||| |||||||||||||| | ||| |
gtacaatcccctgcagcccccctctccggtaattagagggaagcaattacttttccaatcttatgcggttcaattcagcctgtcttgagcttattggtggtgaactataacagGCGTTAAAGACTTATATCTGGCTTCAGTGCTTTGATGGTTCCATTCAGCAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCGTGAAATTG---
upper sequence: GLYMA16G30080.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G055785_T01 (Zea mays), 3'ss of exon 2
tatcgtgttgttctgaaatttacaacatggtaaagtcaagtttattgttgttcc--ctgggtagctagtt---tgttgatttcactctacctttggcatgcttag-
|| | | | | ||| | | | || || ||| | || | | |||||| || | | | || | | |||| | || ||||||||||| | |||||||| || || ||||| ||||| ||||| || ||||| |||||||||||||| |||||| |
----gtaataaaaccagaggttcaattccctgcacccttcttagctgcaactccgctctgttaattcatcctatgttgagtttattggtggtgaactataatagGTGTTGAAGACATATATCTGGCTTCAGTGCTTTGATGGTTCCATACAACAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCAGGAAATTG---
upper sequence: GLYMA16G30080.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0050g00720.t01 (Vitis vinifera), 3'ss of exon 2
--tatcgtgttgttctgaaatttacaacatggtaaagtcaagtttattgttgttccctgggtagctag-tttgttgatttcactctacctttggcatgcttagATGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTAGAGGAAGAGGTAGCCATGTTTTGCCCCATGATATGCCAGGAAGTACTTC
| | | || || ||| | ||| | | || || | | || ||| | | ||| || |||| | | || | | ||||||| || || |||||||| ||||||| |||||||||||||| ||||| || |||||||| ||||||||||||||||||||||||| ||| ||||||
tttgataggctatt-tggtttttgttatatgatgtactcttattcactctttatccttttcttatggcctttatttattttgtttaaaatt--gtgtatcaagATGAAGTCTTATATCTGGCTCCAAACTGCTGATGGTTCTATTCAACAAGTTGAAGAAGAGGTTGCCATGTTTTGCCCCATGATATGCCGAGAAATACTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttgttccctgggtagctagtttgttgatttcactctacctttggcatgcttagATGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTAGAGGAAGAGGTAGCCATGTTTTGCCCCATGATATGCCAGGAAGTACTTC
tgttgat putative branch site (score: 4)
ttgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatcgtgttgttctgaaatttacaacatggtaaagtcaagtttattgttgttccctgggtagctagtttgttgatttcactctacctttggcatgcttagATGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTAGAGGAAGAGGTAGCCATGTTTTGCCCCATGATATGCCAGGAAGTACTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG